2XN9 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE TERNARY COMPLEX BETWEEN HUMAN T CELL RECEPTOR, STAPHYLOCOCCAL ENTEROTOXIN H AND HUMAN MAJOR HISTOCOMPATIBILITY COMPLEX CLASS II

Authors :   M. Saline, K. E. J. Rodstrom, G. Fischer, V. Y. Orekhov, B. G. Karlsson, K. Lindkvist-Petersson

Date :   31 Jul 10 (Deposition) - 24 Nov 10 (Release) - 03 Aug 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym./Biol. Unit : A,B,C,D,E,F

Keywords :   Immune System, Superantigen, Immunoreceptors, Ternary Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Saline, K. E. J. Rodstrom, G. Fischer, V. Y. Orekhov, B. G. Karlsson, K. Lindkvist-Petersson
The Structure Of Superantigen Complexed With Tcr And Mhc Reveals Novel Insights Into Superantigenic T Cell Activation.
Nat. Commun. V. 1 119 2010
PubMed-ID: 21081917 | Reference-DOI: 10.1038/NCOMMS1117

Molecule 1 - T CELL RECEPTOR ALPHA CHAIN C REGION
	Cell	:	T LYMPHOCYTE
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGMT7
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Fragment	:	EXTRACELLULAR DOMAIN, RESIDUES 1-95
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	VARIABLE DOMAIN TRAV27 FUSED TO CONSTANT DOMAIN

Molecule 2 - T CELL RECEPTOR BETA-1 CHAIN C REGION
	Cell	:	T LYMPHOCYTE
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGMT7
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Fragment	:	EXTRACELLULAR DOMAIN, RESIDUES 1-130
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	VARIABLE DOMAIN TRBV19 FUSED TO CONSTANT DOMAIN

Molecule 3 - ENTEROTOXIN H
	Chains	:	C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	K-12
	Expression System Taxid	:	83333
	Expression System Variant	:	UL635
	Organism Scientific	:	STAPHYLOCOCCUS AUREUS
	Organism Taxid	:	1280
	Synonym	:	SEH, STAPHYLOCOCCAL ENTEROTOXIN H

Molecule 4 - HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DR ALPHA CHAIN,
	Cell	:	ANTIGEN PRESENTING CELL
	Chains	:	D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PLM1
	Expression System Strain	:	BL21(DE3)PLYS
	Expression System Taxid	:	469008
	Fragment	:	EXTRACELLULAR DOMAIN, RESIDUES 26-207
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	CHAIN DR 0101
	Synonym	:	MAJOR HISTOCOMPATIBILITY COMPLEX CLASS II ALPHA, MHC CLASS II ANTIGEN DRA CHAIN

Molecule 5 - MAJOR HISTOCOMPATIBILITY COMPLEX CLASS II BETA CHAIN
	Cell	:	ANTIGEN PRESENTING CELL
	Chains	:	E
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PLM1
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Fragment	:	EXTRACELLULAR DOMAIN, RESIDUES 30-219
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	CHAIN DRB1 0101
	Synonym	:	MHC CLASS II ANTIGEN DRB1.1, DR-1, DR1

Molecule 6 - HEMAGGLUTININ
	Chains	:	F
	Fragment	:	RESIDUES 59-71
	Organism Scientific	:	INFLUENZA A VIRUS
	Organism Taxid	:	11320
	Synonym	:	INFLUENZA HEMAGGLUTININ PEPTIDE
	Synthetic	:	YES

		1	2	3	4	5	6
Asymmetric/Biological Unit	:	A	B	C	D	E	F

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 5)

No.	Name	Count	Type	Full Name
1	GOL	4	Ligand/Ion	GLYCEROL
2	NA	1	Ligand/Ion	SODIUM ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:2030 , HIS C:23 , SER C:77 , HOH C:2011 , HOH C:2028	BINDING SITE FOR RESIDUE NA C1216
2	AC2	SOFTWARE	GLU A:17 , ARG A:163 , SER A:164 , HOH A:2092 , SER B:168 , ARG B:195 , GOL B:1245	BINDING SITE FOR RESIDUE GOL A1201
3	AC3	SOFTWARE	GLU A:17 , GOL A:1201 , HOH A:2092 , VAL B:196 , SER B:197	BINDING SITE FOR RESIDUE GOL B1245
4	AC4	SOFTWARE	ARG B:110 , ASP B:153 , GLN B:175 , PRO B:176 , TYR B:188	BINDING SITE FOR RESIDUE GOL B1246
5	AC5	SOFTWARE	ASN B:30 , HIS B:31 , ASP B:32 , SER B:97 , ARG B:98	BINDING SITE FOR RESIDUE GOL B1247

Asymmetric/Biological Unit

No.	Residues
1	A:23	-	A:89
2	A:133	-	A:183
3	A:158	-	B:171
4	B:25	-	B:93
5	B:145	-	B:210
6	C:82	-	C:92
7	D:107	-	D:163
8	E:15	-	E:79
9	E:117	-	E:173

Asymmetric/Biological Unit

No.	Residues
1	Ser A:7	-	Pro A:8
2	Ser B:9	-	Pro B:10
3	Tyr B:151	-	Pro B:152
4	Ala B:243	-	Asp B:244
5	Asn D:15	-	Pro D:16
6	Thr D:113	-	Pro D:114
7	Pro E:108	-	Leu E:109
8	Tyr E:123	-	Pro E:124

Asymmetric/Biological Unit (25, 25)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
01	UniProt	VAR_033379	R	33	K	2B11_HUMAN	Polymorphism	34716432	E	R	4	K
02	UniProt	VAR_033380	R	33	Q	2B11_HUMAN	Polymorphism	34716432	E	R	4	Q
03	UniProt	VAR_016740	Q	39	E	2B11_HUMAN	Polymorphism	---	E	Q	10	E
04	UniProt	VAR_033381	S	66	Y	2B11_HUMAN	Polymorphism	16822820	E	S	37	Y
05	UniProt	VAR_016741	G	74	R	2B11_HUMAN	Polymorphism	---	E	G	45	R
06	UniProt	VAR_033382	Y	76	F	2B11_HUMAN	Polymorphism	1060346	E	Y	47	F
07	UniProt	VAR_033383	Y	89	S	2B11_HUMAN	Polymorphism	36074728	E	Y	60	S
08	UniProt	VAR_016710	L	96	I	2B11_HUMAN	Polymorphism	---	E	L	67	I
09	UniProt	VAR_016711	Q	99	D	2B11_HUMAN	Polymorphism	---	E	Q	70	D
10	UniProt	VAR_033384	Q	99	E	2B11_HUMAN	Polymorphism	17881965	E	Q	70	E
11	UniProt	VAR_033385	Q	99	H	2B11_HUMAN	Polymorphism	17879599	E	Q	70	H
12	UniProt	VAR_016742	R	100	A	2B11_HUMAN	Polymorphism	---	E	R	71	A
13	UniProt	VAR_016712	R	100	E	2B11_HUMAN	Polymorphism	---	E	R	71	E
14	UniProt	VAR_033386	A	102	G	2B11_HUMAN	Polymorphism	17878857	E	A	73	G
15	UniProt	VAR_033387	A	103	E	2B11_HUMAN	Polymorphism	16822805	E	A	74	E
16	UniProt	VAR_016713	T	106	N	2B11_HUMAN	Polymorphism	16822752	E	T	77	N
17	UniProt	VAR_033388	Y	107	H	2B11_HUMAN	Polymorphism	16822512	E	Y	78	H
18	UniProt	VAR_016714	V	114	A	2B11_HUMAN	Polymorphism	17424145	E	V	85	A
19	UniProt	VAR_016715	G	115	V	2B11_HUMAN	Polymorphism	2230810	E	G	86	V
20	UniProt	VAR_033389	G	164	D	2B11_HUMAN	Polymorphism	1059633	E	G	135	D
21	UniProt	VAR_033390	A	169	T	2B11_HUMAN	Polymorphism	2308768	E	A	140	T
22	UniProt	VAR_033391	V	171	M	2B11_HUMAN	Polymorphism	701829	E	V	142	M
23	UniProt	VAR_033392	Q	178	H	2B11_HUMAN	Polymorphism	701830	E	Q	149	H
24	UniProt	VAR_033393	R	195	Q	2B11_HUMAN	Polymorphism	3205588	E	R	166	Q
25	UniProt	VAR_033394	T	210	I	2B11_HUMAN	Polymorphism	17423930	E	T	181	I

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric/Biological Unit (2, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	STAPH_STREP_TOXIN_2	PS00278	Staphyloccocal enterotoxin/Streptococcal pyrogenic exotoxin signature 2.	ETXH_STAAU	154-177	1	C:130-153
2	IG_MHC	PS00290	Immunoglobulins and major histocompatibility complex proteins signature.	DRA_HUMAN	186-192	1	D:161-167
2	IG_MHC	PS00290		2B11_HUMAN	200-206	1	E:171-177

Asymmetric/Biological Unit (7, 7)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.3	ENST00000360004	3	ENSE00001930619	chr6:32557625-32557420	206	2B11_HUMAN	1-34	34	1	E:2-5	4
1.4	ENST00000360004	4	ENSE00001731226	chr6:32552155-32551886	270	2B11_HUMAN	34-124	91	1	E:5-95	91
1.5b	ENST00000360004	5b	ENSE00001801024	chr6:32549615-32549334	282	2B11_HUMAN	124-218	95	1	E:95-189	95
1.6	ENST00000360004	6	ENSE00001717727	chr6:32548633-32548523	111	2B11_HUMAN	218-255	38	1	E:189-189	1
1.7	ENST00000360004	7	ENSE00001773376	chr6:32548047-32548024	24	2B11_HUMAN	255-263	9	0	-	-
1.8	ENST00000360004	8	ENSE00001954617	chr6:32546881-32546546	336	2B11_HUMAN	263-266	4	0	-	-

2.6a	ENST00000383259	6a	ENSE00001839042	HSCHR6_MHC_QBL:32365090-32365280	191	DRA_HUMAN	1-28	28	0	-	-
2.7b	ENST00000383259	7b	ENSE00001719010	HSCHR6_MHC_QBL:32367694-32367939	246	DRA_HUMAN	28-110	83	1	D:4-85	82
2.8c	ENST00000383259	8c	ENSE00001737588	HSCHR6_MHC_QBL:32368431-32368712	282	DRA_HUMAN	110-204	95	1	D:85-179	95
2.9a	ENST00000383259	9a	ENSE00001770912	HSCHR6_MHC_QBL:32369002-32369167	166	DRA_HUMAN	204-254	51	1	D:179-181	3
2.10b	ENST00000383259	10b	ENSE00001925700	HSCHR6_MHC_QBL:32369906-32370300	395	DRA_HUMAN	-	0	0	-	-

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:199
 aligned with TCA_HUMAN | P01848 from UniProtKB/Swiss-Prot  Length:142

    Alignment length:199
                                                                                                                                        1                                                                                          
                                     -         -         -         -         -         -         -         -         -         -        |2        12        22        32        42        52        62        72        82         
            TCA_HUMAN     - ------------------------------------------------------------------------------------------------------------PNIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKTVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPEDTFFPS  91
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------DUF1968-2xn9A01 A:117-200                                                            Pfam domains
         Sec.struct. author ...eee..eeeee....eeeeee.......eeeeee......eeeeee.....eeee..eeeee.....eeeeee...hhhhheeeeeee.......ee...eeeeee..........................................eee...eeeeehhhheeeeeeeeee.....hhhhhh............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xn9 A   2 QLLEQSPQFLSIQEGENLTVYCNSSSVFSSLQWYRQEPGEGPVLLVTVVTGGEVKKLKRLTFQFGDARKDSSLHITAAQPGDTGLYLCAGAGSQGNLIFGKGTKLSVKPNIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPEDTFFPS 200
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191

Chain B from PDB  Type:PROTEIN  Length:242
 aligned with TRBC1_HUMAN | P01850 from UniProtKB/Swiss-Prot  Length:177

    Alignment length:242
                                                                                                                                            1                                                                                                                                 
                                     -         -         -         -         -         -         -         -         -         -         -  |      8        18        28        38        48        58        68        78        88        98       108       118       128  
          TRBC1_HUMAN     - ----------------------------------------------------------------------------------------------------------------EDLNKVFPPEVAVFEPSEAEISHTQKATLVCLATGFFPDHVELSWWVNGKEVHSGVSTDPQPLKEQPALNDSRYCLSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRAD 130
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------C1-set-2xn9B01 B:129-222                                                                      ---------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee.....eeeeeeee...eeeeeeeeee..eeee......eee.........eee........eeeeeeee.......ee...eeeeee.hhhhh..........hhhhhhhhh...............eeeeeee..eee...eee....ee.........eeeeeeeeeehhhhh....eeeeeeee..................eeeeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xn9 B   3 DGGITQSPKYLFRKEGQNVTLSCEQNLNHDAMYWYRQDPGQGLRLIYYSQIVNDFQKGDIAEGYSVSREKKESFPLTVTSAQKNPTAFYLCASSSRSSYEQYFGPGTRLTVTEDLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALNDSRYSLSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRAD 244
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242

Chain C from PDB  Type:PROTEIN  Length:215
 aligned with ETXH_STAAU | P0A0M0 from UniProtKB/Swiss-Prot  Length:241

    Alignment length:215
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234     
           ETXH_STAAU    25 EDLHDKSELTDLALANAYGQYNHPFIKENIKSDEISGEKDLIFRNQGDSGNDLRVKFATADLAQKFKNKNVDIYGASFYYKCEKISENISECLYGGTTLNSEKLAQERVIGANVWVDGIQKETELIRTNKKNVTLQELDIKIRKILSDKYKIYYKDSEISKGLIEFDMKTPRDYSFDIYDLKGENDYEIDKIYEDNKTLKSDDISHIDVNLYTKK 239
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------Stap_Strp_toxin-2xn9C02 C:13-100                                                        -------Stap_Strp_tox_C-2xn9C01 C:108-212                                                                        --- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhh.eeeeee....ee...eeee...hhhhheeeee..hhhhhhhhh...eeeee.ee...........eeeee..eee...eeeeeeeeeeeeee..ee...eeeeeee.eeehhhhhhhhhhhhhhhhh.........eeeeeeee.....eeee.......hhhhhhhhhh...eee...eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------STAPH_STREP_TOXIN_2     -------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xn9 C   1 EDLHDKSELTDLALANAYGQYNHPFIKENIKSDEISGEKDLIFRNQGDSGNDLRVKFATADLAQKFKNKNVDIYGASFYYKCEKISENISECLYGGTTLNSEKLAQERVIGANVWVDGIQKETELIRTNKKNVTLQELDIKIRKILSDKYKIYYKDSEISKGLIEFDMKTPRDYSFDIYDLKGENDYEIDKIYEDNKTLKSDDISHIDVNLYTKK 215
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

Chain D from PDB  Type:PROTEIN  Length:178
 aligned with DRA_HUMAN | P01903 from UniProtKB/Swiss-Prot  Length:254

    Alignment length:178
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198        
            DRA_HUMAN    29 EHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGALANIAVDKANLEIMTKRSNYTPITNVPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVTWLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCRVEHWGLDEPLLKHWEFD 206
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains MHC_II_alpha-2xn9D02 D:4-84                                                      --------C1-set-2xn9D01 D:93-175                                                            ------ Pfam domains
         Sec.struct. author .eeeeeeeeeee...eeeeeeee..eeeeeee....eeee...hhhhhh..hhhhhhhhhhhhhhhhhhhhhhh..........eeeeee.........eeeeeeeeee.....eeeeee..eee....ee...ee.....eeeeeeeee......eeeeeee.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC -------------- PROSITE
           Transcript 2 (1) Exon 2.7b  PDB: D:4-85 UniProt: 28-110 [INCOMPLETE]                               ---------------------------------------------------------------------------------------------2.9 Transcript 2 (1)
           Transcript 2 (2) ---------------------------------------------------------------------------------Exon 2.8c  PDB: D:85-179 UniProt: 110-204                                                      -- Transcript 2 (2)
                 2xn9 D   4 EHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGALANIAVDKANLEIMTKRSNYTPITNVPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVTWLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCRVEHWGLDEPLLKHWEFD 181
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173

Chain E from PDB  Type:PROTEIN  Length:188
 aligned with 2B11_HUMAN | P04229 from UniProtKB/Swiss-Prot  Length:266

    Alignment length:188
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210        
           2B11_HUMAN    31 DTRPRFLWQLKFECHFFNGTERVRLLERCIYNQEESVRFDSDVGEYRAVTELGRPDAEYWNSQKDLLEQRRAAVDTYCRHNYGVGESFTVQRRVEPKVTVYPSKTQPLQHHNLLVCSVSGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPSVTSPLTVEWR 218
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----------MHC_II_beta-2xn9E02 E:13-87                                                ---------------C1-set-2xn9E01 E:103-185                                                           ---- Pfam domains
         Sec.struct. author .....eeeeeeeeeeee....eeeeeeeeee..eeeeeee.....eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeee.........eeeeeeeeee.....eeeeee..eee...eee...ee.....eeeeeeeee.......eeeeee.......eeeee. Sec.struct. author
             SAPs(SNPs) (1) --K-----E--------------------------Y-------R-F------------S------I--DA-GE--NH------AV------------------------------------------------D----T-M------H----------------Q--------------I-------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) --Q-----------------------------------------------------------------EE---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (2)
             SAPs(SNPs) (3) --------------------------------------------------------------------H----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (3)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC ------------ PROSITE
           Transcript 1 (1) 1.3 -----------------------------------------------------------------------------------------Exon 1.5b  PDB: E:95-189 UniProt: 124-218                                                       Transcript 1 (1)
           Transcript 1 (2) ---Exon 1.4  PDB: E:5-95 UniProt: 34-124                                                      ---------------------------------------------------------------------------------------------1 Transcript 1 (2)
                 2xn9 E   2 DTRPRFLWQLKFECHFFNGTERVRLLERCIYNQEESVRFDSDVGEYRAVTELGRPDAEYWNSQKDLLEQRRAAVDTYCRHNYGVGESFTVQRRVEPKVTVYPSKTQPLQHHNLLVCSVSGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPSVTSPLTVEWR 189
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181

Chain F from PDB  Type:PROTEIN  Length:13
 aligned with A8CDU0_9INFA | A8CDU0 from UniProtKB/TrEMBL  Length:104

    Alignment length:13
                                    68   
         A8CDU0_9INFA    59 PKYVKQNTLKLAT  71
               SCOP domains ------------- SCOP domains
               CATH domains ------------- CATH domains
               Pfam domains Hemagglutinin Pfam domains
         Sec.struct. author ............. Sec.struct. author
                 SAPs(SNPs) ------------- SAPs(SNPs)
                    PROSITE ------------- PROSITE
                 Transcript ------------- Transcript
                 2xn9 F   1 PKYVKQNTLKLAT  13
                                    10

Chain F from PDB  Type:PROTEIN  Length:13
 aligned with HEMA_I89A7 | Q03909 from UniProtKB/Swiss-Prot  Length:571

    Alignment length:13
                                   336   
           HEMA_I89A7   327 PKYVKQNTLKLAT 339
               SCOP domains ------------- SCOP domains
               CATH domains ------------- CATH domains
               Pfam domains Hemagglutinin Pfam domains
         Sec.struct. author ............. Sec.struct. author
                 SAPs(SNPs) ------------- SAPs(SNPs)
                    PROSITE ------------- PROSITE
                 Transcript ------------- Transcript
                 2xn9 F   1 PKYVKQNTLKLAT  13
                                    10

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

(no "SCOP Domain" information available for 2XN9)

(no "CATH Domain" information available for 2XN9)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (TCA_HUMAN | P01848)

biological process
	GO:0031295	T cell costimulation	The process of providing, via surface-bound receptor-ligand pairs, a second, antigen-independent, signal in addition to that provided by the T cell receptor to augment T cell activation.
	GO:0050852	T cell receptor signaling pathway	A series of molecular signals initiated by the cross-linking of an antigen receptor on a T cell.
	GO:0050776	regulation of immune response	Any process that modulates the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.
cellular component
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Chain B (TRBC1_HUMAN | P01850)

biological process
	GO:0031295	T cell costimulation	The process of providing, via surface-bound receptor-ligand pairs, a second, antigen-independent, signal in addition to that provided by the T cell receptor to augment T cell activation.
	GO:0050852	T cell receptor signaling pathway	A series of molecular signals initiated by the cross-linking of an antigen receptor on a T cell.
	GO:0006955	immune response	Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
	GO:0050776	regulation of immune response	Any process that modulates the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.
cellular component
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Chain C (ETXH_STAAU | P0A0M0)

molecular function
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
biological process
	GO:0009405	pathogenesis	The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
cellular component
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

Chain D (DRA_HUMAN | P01903)

molecular function
	GO:0023026	MHC class II protein complex binding	Interacting selectively and non-covalently with the class II major histocompatibility complex.
	GO:0032395	MHC class II receptor activity	Combining with an MHC class II protein complex and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity.
	GO:0042605	peptide antigen binding	Interacting selectively and non-covalently with an antigen peptide.
biological process
	GO:0031295	T cell costimulation	The process of providing, via surface-bound receptor-ligand pairs, a second, antigen-independent, signal in addition to that provided by the T cell receptor to augment T cell activation.
	GO:0050852	T cell receptor signaling pathway	A series of molecular signals initiated by the cross-linking of an antigen receptor on a T cell.
	GO:0019882	antigen processing and presentation	The process in which an antigen-presenting cell expresses antigen (peptide or lipid) on its cell surface in association with an MHC protein complex.
	GO:0019886	antigen processing and presentation of exogenous peptide antigen via MHC class II	The process in which an antigen-presenting cell expresses a peptide antigen of exogenous origin on its cell surface in association with an MHC class II protein complex. The peptide antigen is typically, but not always, processed from a whole protein.
	GO:0002504	antigen processing and presentation of peptide or polysaccharide antigen via MHC class II	The process in which an antigen-presenting cell expresses antigen (peptide or polysaccharide) on its cell surface in association with an MHC class II protein complex.
	GO:0050890	cognition	The operation of the mind by which an organism becomes aware of objects of thought or perception; it includes the mental activities associated with thinking, learning, and memory.
	GO:0006955	immune response	Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
	GO:0002376	immune system process	Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
	GO:0060333	interferon-gamma-mediated signaling pathway	A series of molecular signals initiated by the binding of interferon-gamma to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription. Interferon gamma is the only member of the type II interferon found so far.
	GO:0002503	peptide antigen assembly with MHC class II protein complex	The binding of a peptide to the antigen binding groove of an MHC class II protein complex.
	GO:0002506	polysaccharide assembly with MHC class II protein complex	The binding of a polysaccharide to the antigen binding groove of an MHC class II protein complex.
	GO:0016032	viral process	A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
	GO:0012507	ER to Golgi transport vesicle membrane	The lipid bilayer surrounding a vesicle transporting substances from the endoplasmic reticulum to the Golgi.
	GO:0005794	Golgi apparatus	A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
	GO:0000139	Golgi membrane	The lipid bilayer surrounding any of the compartments of the Golgi apparatus.
	GO:0042613	MHC class II protein complex	A transmembrane protein complex composed of an MHC class II alpha and MHC class II beta chain, and with or without a bound peptide or polysaccharide antigen.
	GO:0009986	cell surface	The external part of the cell wall and/or plasma membrane.
	GO:0030669	clathrin-coated endocytic vesicle membrane	The lipid bilayer surrounding a clathrin-coated endocytic vesicle.
	GO:0030666	endocytic vesicle membrane	The lipid bilayer surrounding an endocytic vesicle.
	GO:0005783	endoplasmic reticulum	The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
	GO:0005789	endoplasmic reticulum membrane	The lipid bilayer surrounding the endoplasmic reticulum.
	GO:0005768	endosome	A vacuole to which materials ingested by endocytosis are delivered.
	GO:0010008	endosome membrane	The lipid bilayer surrounding an endosome.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0071556	integral component of lumenal side of endoplasmic reticulum membrane	The component of the endoplasmic reticulum membrane consisting of the gene products that penetrate only the lumenal side of the membrane.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0005887	integral component of plasma membrane	The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0031902	late endosome membrane	The lipid bilayer surrounding a late endosome.
	GO:0005765	lysosomal membrane	The lipid bilayer surrounding the lysosome and separating its contents from the cell cytoplasm.
	GO:0005764	lysosome	A small lytic vacuole that has cell cycle-independent morphology and is found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
	GO:0032588	trans-Golgi network membrane	The lipid bilayer surrounding any of the compartments that make up the trans-Golgi network.
	GO:0030658	transport vesicle membrane	The lipid bilayer surrounding a transport vesicle.

Chain E (2B11_HUMAN | P04229)

molecular function
	GO:0023026	MHC class II protein complex binding	Interacting selectively and non-covalently with the class II major histocompatibility complex.
	GO:0042605	peptide antigen binding	Interacting selectively and non-covalently with an antigen peptide.
	GO:0001618	virus receptor activity	Combining with a virus component and mediating entry of the virus into the cell.
biological process
	GO:0031295	T cell costimulation	The process of providing, via surface-bound receptor-ligand pairs, a second, antigen-independent, signal in addition to that provided by the T cell receptor to augment T cell activation.
	GO:0050852	T cell receptor signaling pathway	A series of molecular signals initiated by the cross-linking of an antigen receptor on a T cell.
	GO:0042088	T-helper 1 type immune response	An immune response which is associated with resistance to intracellular bacteria, fungi, and protozoa, and pathological conditions such as arthritis, and which is typically orchestrated by the production of particular cytokines by T-helper 1 cells, most notably interferon-gamma, IL-2, and lymphotoxin.
	GO:0019882	antigen processing and presentation	The process in which an antigen-presenting cell expresses antigen (peptide or lipid) on its cell surface in association with an MHC protein complex.
	GO:0019886	antigen processing and presentation of exogenous peptide antigen via MHC class II	The process in which an antigen-presenting cell expresses a peptide antigen of exogenous origin on its cell surface in association with an MHC class II protein complex. The peptide antigen is typically, but not always, processed from a whole protein.
	GO:0002504	antigen processing and presentation of peptide or polysaccharide antigen via MHC class II	The process in which an antigen-presenting cell expresses antigen (peptide or polysaccharide) on its cell surface in association with an MHC class II protein complex.
	GO:0016045	detection of bacterium	The series of events in which a stimulus from a bacterium is received and converted into a molecular signal.
	GO:0002455	humoral immune response mediated by circulating immunoglobulin	An immune response dependent upon secreted immunoglobulin. An example of this process is found in Mus musculus.
	GO:0006955	immune response	Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
	GO:0002376	immune system process	Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
	GO:0002381	immunoglobulin production involved in immunoglobulin mediated immune response	The appearance of immunoglobulin due to biosynthesis or secretion following a cellular stimulus during an immune response, resulting in an increase in its intracellular or extracellular levels.
	GO:0002437	inflammatory response to antigenic stimulus	An inflammatory response to an antigenic stimulus, which can be include any number of T cell or B cell epitopes.
	GO:0060333	interferon-gamma-mediated signaling pathway	A series of molecular signals initiated by the binding of interferon-gamma to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription. Interferon gamma is the only member of the type II interferon found so far.
	GO:0042130	negative regulation of T cell proliferation	Any process that stops, prevents or reduces the rate or extent of T cell proliferation.
	GO:0032689	negative regulation of interferon-gamma production	Any process that stops, prevents, or reduces the frequency, rate, or extent of interferon-gamma production. Interferon-gamma is also known as type II interferon.
	GO:0035774	positive regulation of insulin secretion involved in cellular response to glucose stimulus	Any process that increases the frequency, rate or extent of the regulated release of insulin that contributes to the response of a cell to glucose.
	GO:0051262	protein tetramerization	The formation of a protein tetramer, a macromolecular structure consisting of four noncovalently associated identical or nonidentical subunits.
	GO:2001179	regulation of interleukin-10 secretion	Any process that modulates the frequency, rate or extent of interleukin-10 secretion.
	GO:0032673	regulation of interleukin-4 production	Any process that modulates the frequency, rate, or extent of interleukin-4 production.
	GO:0046718	viral entry into host cell	The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
	GO:0016032	viral process	A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
	GO:0012507	ER to Golgi transport vesicle membrane	The lipid bilayer surrounding a vesicle transporting substances from the endoplasmic reticulum to the Golgi.
	GO:0005794	Golgi apparatus	A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
	GO:0000139	Golgi membrane	The lipid bilayer surrounding any of the compartments of the Golgi apparatus.
	GO:0042613	MHC class II protein complex	A transmembrane protein complex composed of an MHC class II alpha and MHC class II beta chain, and with or without a bound peptide or polysaccharide antigen.
	GO:0030669	clathrin-coated endocytic vesicle membrane	The lipid bilayer surrounding a clathrin-coated endocytic vesicle.
	GO:0030666	endocytic vesicle membrane	The lipid bilayer surrounding an endocytic vesicle.
	GO:0005783	endoplasmic reticulum	The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
	GO:0005789	endoplasmic reticulum membrane	The lipid bilayer surrounding the endoplasmic reticulum.
	GO:0005768	endosome	A vacuole to which materials ingested by endocytosis are delivered.
	GO:0010008	endosome membrane	The lipid bilayer surrounding an endosome.
	GO:0009897	external side of plasma membrane	The leaflet of the plasma membrane that faces away from the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0071556	integral component of lumenal side of endoplasmic reticulum membrane	The component of the endoplasmic reticulum membrane consisting of the gene products that penetrate only the lumenal side of the membrane.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0031902	late endosome membrane	The lipid bilayer surrounding a late endosome.
	GO:0005765	lysosomal membrane	The lipid bilayer surrounding the lysosome and separating its contents from the cell cytoplasm.
	GO:0005764	lysosome	A small lytic vacuole that has cell cycle-independent morphology and is found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
	GO:0032588	trans-Golgi network membrane	The lipid bilayer surrounding any of the compartments that make up the trans-Golgi network.
	GO:0030658	transport vesicle membrane	The lipid bilayer surrounding a transport vesicle.

Chain F (A8CDU0_9INFA | A8CDU0)

molecular function
	GO:0046789	host cell surface receptor binding	Interacting selectively and non-covalently with a receptor on the host cell surface.
biological process
	GO:0075512	clathrin-dependent endocytosis of virus by host cell	Any clathrin-mediated endocytosis that is involved in the uptake of a virus into a host cell. Begins by invagination of a specific region of the host cell plasma membrane around the bound virus to form a clathrin-coated pit, which then pinches off to form a clathrin-coated endocytic vesicle containing the virus.
	GO:0075509	endocytosis involved in viral entry into host cell	Any endocytosis that is involved in the uptake of a virus into a host cell.
	GO:0039654	fusion of virus membrane with host endosome membrane	Fusion of a virus membrane with a host endosome membrane. Occurs after internalization of the virus through the endosomal pathway, and results in release of the virus contents into the cell.
	GO:0019064	fusion of virus membrane with host plasma membrane	Fusion of a viral membrane with the host cell membrane during viral entry. Results in release of the virion contents into the cytoplasm.
	GO:0039663	membrane fusion involved in viral entry into host cell	Merging of the virion membrane and a host membrane (host plasma membrane or host organelle membrane) that is involved in the uptake of a virus into a host cell.
	GO:0019065	receptor-mediated endocytosis of virus by host cell	Any receptor-mediated endocytosis that is involved in the uptake of a virus into a host cell; successive instances of virus endocytosis result in the accumulation of virus particles within the cell.
	GO:0046718	viral entry into host cell	The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
	GO:0016032	viral process	A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
	GO:0019062	virion attachment to host cell	The process by which a virion protein binds to molecules on the host cellular surface or host cell surface projection.
cellular component
	GO:0033644	host cell membrane	Double layer of lipid molecules as it encloses host cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. The host is defined as the larger of the organisms involved in a symbiotic interaction.
	GO:0020002	host cell plasma membrane	The plasma membrane surrounding a host cell.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0019031	viral envelope	The lipid bilayer of a virion that surrounds the protein capsid. May also contain glycoproteins.
	GO:0019012	virion	The complete fully infectious extracellular virus particle.
	GO:0055036	virion membrane	The lipid bilayer surrounding a virion.

Chain F (HEMA_I89A7 | Q03909)

molecular function
	GO:0046789	host cell surface receptor binding	Interacting selectively and non-covalently with a receptor on the host cell surface.
biological process
	GO:0075512	clathrin-dependent endocytosis of virus by host cell	Any clathrin-mediated endocytosis that is involved in the uptake of a virus into a host cell. Begins by invagination of a specific region of the host cell plasma membrane around the bound virus to form a clathrin-coated pit, which then pinches off to form a clathrin-coated endocytic vesicle containing the virus.
	GO:0075509	endocytosis involved in viral entry into host cell	Any endocytosis that is involved in the uptake of a virus into a host cell.
	GO:0039654	fusion of virus membrane with host endosome membrane	Fusion of a virus membrane with a host endosome membrane. Occurs after internalization of the virus through the endosomal pathway, and results in release of the virus contents into the cell.
	GO:0019064	fusion of virus membrane with host plasma membrane	Fusion of a viral membrane with the host cell membrane during viral entry. Results in release of the virion contents into the cytoplasm.
	GO:0039663	membrane fusion involved in viral entry into host cell	Merging of the virion membrane and a host membrane (host plasma membrane or host organelle membrane) that is involved in the uptake of a virus into a host cell.
	GO:0019065	receptor-mediated endocytosis of virus by host cell	Any receptor-mediated endocytosis that is involved in the uptake of a virus into a host cell; successive instances of virus endocytosis result in the accumulation of virus particles within the cell.
	GO:0046718	viral entry into host cell	The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
	GO:0016032	viral process	A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
	GO:0019062	virion attachment to host cell	The process by which a virion protein binds to molecules on the host cellular surface or host cell surface projection.
cellular component
	GO:0033644	host cell membrane	Double layer of lipid molecules as it encloses host cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. The host is defined as the larger of the organisms involved in a symbiotic interaction.
	GO:0020002	host cell plasma membrane	The plasma membrane surrounding a host cell.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0019031	viral envelope	The lipid bilayer of a virion that surrounds the protein capsid. May also contain glycoproteins.
	GO:0019012	virion	The complete fully infectious extracellular virus particle.
	GO:0055036	virion membrane	The lipid bilayer surrounding a virion.

Asymmetric/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		GOL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Ala B:243 - Asp B:244	[ RasMol ]
		Asn D:15 - Pro D:16	[ RasMol ]
		Pro E:108 - Leu E:109	[ RasMol ]
		Ser A:7 - Pro A:8	[ RasMol ]
		Ser B:9 - Pro B:10	[ RasMol ]
		Thr D:113 - Pro D:114	[ RasMol ]
		Tyr B:151 - Pro B:152	[ RasMol ]
		Tyr E:123 - Pro E:124	[ RasMol ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	2xn9
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	2B11_HUMAN \| P04229
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	A8CDU0_9INFA \| A8CDU0
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	DRA_HUMAN \| P01903
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	ETXH_STAAU \| P0A0M0
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	HEMA_I89A7 \| Q03909
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	TCA_HUMAN \| P01848
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	TRBC1_HUMAN \| P01850
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	2B11_HUMAN \| P04229
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	A8CDU0_9INFA \| A8CDU0
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	DRA_HUMAN \| P01903
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	ETXH_STAAU \| P0A0M0
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	HEMA_I89A7 \| Q03909
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	TCA_HUMAN \| P01848
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	TRBC1_HUMAN \| P01850
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

1a6a	THE STRUCTURE OF AN INTERMEDIATE IN CLASS II MHC MATURATION: CLIP BOUND TO HLA-DR3
1aqd	HLA-DR1 (DRA, DRB1 0101) HUMAN CLASS II HISTOCOMPATIBILITYPROTEIN (EXTRACELLULAR DOMAIN) COMPLEXED WITH ENDOGENOUSPEPTIDE
1bx2	CRYSTAL STRUCTURE OF HLA-DR2 (DRA0101, DRB11501) COMPLEXEDWITH A PEPTIDE FROM HUMAN MYELIN BASIC PROTEIN
1d5m	X-RAY CRYSTAL STRUCTURE OF HLA-DR4 COMPLEXED WITH PEPTIDE
1d5x	X-RAY CRYSTAL STRUCTURE OF HLA-DR4 COMPLEXED WITH DIPEPTIDE MIMETIC
1d5z	X-RAY CRYSTAL STRUCTURE OF HLA-DR4 COMPLEXED WITH PEPTIDOMIMETIC
1d6e	CRYSTAL STRUCTURE OF HLA-DR4 COMPLEX WITH PEPTIDOMIMETIC AND SEB
1dlh
1enf	CRYSTAL STRUCTURE OF STAPHYLOCOCCAL ENTEROTOXIN H DETERMINED TO 1.69 A RESOLUTION
1ewc	CRYSTAL STRUCTURE OF ZN2+ LOADED STAPHYLOCOCCAL ENTEROTOXIN H
1f77	STAPHYLOCOCCAL ENTEROTOXIN H DETERMINED TO 2. 4 A RESOLUTION
1fv1	STRUCTURAL BASIS FOR THE BINDING OF AN IMMUNODOMINANTPEPTIDE FROM MYELIN BASIC PROTEIN IN DIFFERENT REGISTERS BYTWO HLA-DR2 ALLELES
1fyt	CRYSTAL STRUCTURE OF A COMPLEX OF A HUMAN ALPHA/BETA-T CELLRECEPTOR, INFLUENZA HA ANTIGEN PEPTIDE, AND MHC CLASS IIMOLECULE, HLA-DR1
1h15	X-RAY CRYSTAL STRUCTURE OF HLA-DRA10101/ DRB50101 COMPLEXED WITH A PEPTIDE FROM EPSTEIN BARR VIRUS DNA POLYMERASE.
1hqr	CRYSTAL STRUCTURE OF A SUPERANTIGEN BOUND TO THE HIGH- AFFINITY, ZINC-DEPENDENT SITE ON MHC CLASS II
1hxy	CRYSTAL STRUCTURE OF STAPHYLOCOCCAL ENTEROTOXIN H INCOMPLEX WITH HUMAN MHC CLASS II
1j8h	CRYSTAL STRUCTURE OF A COMPLEX OF A HUMAN ALPHA/BETA-T CELLRECEPTOR, INFLUENZA HA ANTIGEN PEPTIDE, AND MHC CLASS IIMOLECULE, HLA-DR4
1jwm	CRYSTAL STRUCTURE OF THE COMPLEX OF THE MHC CLASS IIMOLECULE HLA-DR1(HA PEPTIDE 306-318) WITH THE SUPERANTIGENSEC3
1jws	CRYSTAL STRUCTURE OF THE COMPLEX OF THE MHC CLASS IIMOLECULE HLA-DR1 (HA PEPTIDE 306-318) WITH THESUPERANTIGEN SEC3 VARIANT 3B1
1jwu	CRYSTAL STRUCTURE OF THE COMPLEX OF THE MHC CLASS IIMOLECULE HLA-DR1 (HA PEPTIDE 306-318) WITH THESUPERANTIGEN SEC3 VARIANT 3B2
1kg0	STRUCTURE OF THE EPSTEIN-BARR VIRUS GP42 PROTEIN BOUND TOTHE MHC CLASS II RECEPTOR HLA-DR1
1kgc	IMMUNE RECEPTOR
1klg	CRYSTAL STRUCTURE OF HLA-DR1/TPI(23-37, THR28-->ILE MUTANT) COMPLEXED WITH STAPHYLOCOCCAL ENTEROTOXIN C3 VARIANT 3B2(SEC3 -3B2)
1klu	CRYSTAL STRUCTURE OF HLA-DR1/TPI(23-37) COMPLEXED WITHSTAPHYLOCOCCAL ENTEROTOXIN C3 VARIANT 3B2 (SEC3-3B2)
1ktk	COMPLEX OF STREPTOCOCCAL PYROGENIC ENTEROTOXIN C (SPEC)WITH A HUMAN T CELL RECEPTOR BETA CHAIN (VBETA2.1)
1lo5	CRYSTAL STRUCTURE OF THE D227A VARIANT OF STAPHYLOCOCCALENTEROTOXIN A IN COMPLEX WITH HUMAN MHC CLASS II
1mi5	THE CRYSTAL STRUCTURE OF LC13 TCR IN COMPLEX WITH HLAB8- EBVPEPTIDE COMPLEX
1oga	A STRUCTURAL BASIS FOR IMMUNODOMINANT HUMAN T-CELL RECEPTOR RECOGNITION.
1pyw	HUMAN CLASS II MHC PROTEIN HLA-DR1 BOUND TO A DESIGNEDPEPTIDE RELATED TO INFLUENZA VIRUS HEMAGGLUTININ, FVKQNA(MAA)AL, IN COMPLEX WITH STAPHYLOCOCCAL ENTEROTOXINC3 VARIANT 3B2 (SEC3-3B2)
1qrn	CRYSTAL STRUCTURE OF HUMAN A6 TCR COMPLEXED WITH HLA-A2 BOUND TO ALTERED HTLV-1 TAX PEPTIDE P6A
1r5i	CRYSTAL STRUCTURE OF THE MAM-MHC COMPLEX
1seb	COMPLEX OF THE HUMAN MHC CLASS II GLYCOPROTEIN HLA-DR1 ANDTHE BACTERIAL SUPERANTIGEN SEB
1sje	HLA-DR1 COMPLEXED WITH A 16 RESIDUE HIV CAPSID PEPTIDEBOUND IN A HAIRPIN CONFORMATION
1sjh	HLA-DR1 COMPLEXED WITH A 13 RESIDUE HIV CAPSID PEPTIDE
1t5w	HLA-DR1 IN COMPLEX WITH A SYNTHETIC PEPTIDE(AAYSDQATPLLLSPR)
1t5x	HLA-DR1 IN COMPLEX WITH A SYNTHETIC PEPTIDE(AAYSDQATPLLLSPR) AND THE SUPERANTIGEN SEC3-3B2
1ymm	TCR/HLA-DR2B/MBP-PEPTIDE COMPLEX
1zgl	CRYSTAL STRUCTURE OF 3A6 TCR BOUND TO MBP /HLA-DR2A
2ak4	CRYSTAL STRUCTURE OF SB27 TCR IN COMPLEX WITH HLA-B*3508- 13MER PEPTIDE
2axh	CRYSTAL STRUCTURES OF T CELL RECEPTOR BETA CHAINS RELATEDTO RHEUMATOID ARTHRITIS
2bnq	STRUCTURAL AND KINETIC BASIS FOR HIGHTENED IMMUNOGENICITY OF T CELL VACCINES
2bnr	STRUCTURAL AND KINETIC BASIS FOR HIGHTENED IMMUNOGENICITY OF T CELL VACCINES
2bnu	STRUCTURAL AND KINETIC BASIS FOR HIGHTENED IMMUNOGENICITY OF T CELL VACCINES
2cde	STRUCTURE AND BINDING KINETICS OF THREE DIFFERENT HUMAN CD1D-ALPHA-GALACTOSYLCERAMIDE SPECIFIC T CELL RECEPTORS - INKT-TCR
2cdf	STRUCTURE AND BINDING KINETICS OF THREE DIFFERENT HUMAN CD1D-ALPHA-GALACTOSYLCERAMIDE- SPECIFIC T CELL RECEPTORS (TCR 5E)
2cdg	STRUCTURE AND BINDING KINETICS OF THREE DIFFERENT HUMAN CD1D-ALPHA-GALACTOSYLCERAMIDE- SPECIFIC T CELL RECEPTORS (TCR 5B)
2esv	STRUCTURE OF THE HLA-E-VMAPRTLIL/KK50.4 TCR COMPLEX
2eyr	A STRUCTURAL BASIS FOR SELECTION AND CROSS- SPECIESREACTIVITY OF THE SEMI-INVARIANT NKT CELL RECEPTOR INCD1D/GLYCOLIPID RECOGNITION
2eys	A STRUCTURAL BASIS FOR SELECTION AND CROSS- SPECIESREACTIVITY OF THE SEMI-INVARIANT NKT CELL RECEPTOR INCD1D/GLYCOLIPID RECOGNITION
2eyt	A STRUCTURAL BASIS FOR SELECTION AND CROSS- SPECIESREACTIVITY OF THE SEMI-INVARIANT NKT CELL RECEPTOR INCD1D/GLYCOLIPID RECOGNITION
2g9h	CRYSTAL STRUCTURE OF STAPHYLOCOCCAL ENTEROTOXIN I (SEI) INCOMPLEX WITH A HUMAN MHC CLASS II MOLECULE
2gj6	THE COMPLEX BETWEEN TCR A6 AND HUMAN CLASS I MHC HLA-A2WITH THE MODIFIED HTLV-1 TAX (Y5K-4-[3-INDOLYL]-BUTYRICACID) PEPTIDE
2seb	X-RAY CRYSTAL STRUCTURE OF HLA-DR4 COMPLEXED WITH A PEPTIDE FROM HUMAN COLLAGEN II
2wbj	TCR COMPLEX
2xna	CRYSTAL STRUCTURE OF THE TERNARY COMPLEX BETWEEN HUMAN T CELL RECEPTOR AND STAPHYLOCOCCAL ENTEROTOXIN H

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 5)

Sites (5, 5)

SS Bonds (9, 9)

Cis Peptide Bonds (8, 8)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (25, 25)

PROSITE Motifs (2, 3)

Exons (7, 7)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (7, 9)

Gene Ontology (68, 132)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File