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

Asym./Biol. Unit (Jmol Viewer)

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

Title :   TCR/HLA-DR2B/MBP-PEPTIDE COMPLEX

Authors :   M. Hahn, M. J. Nicholson, J. Pyrdol, K. W. Wucherpfennig

Date :   21 Jan 05 (Deposition) - 03 May 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.50

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

Keywords :   Protein-Protein Complex, T Cell Repertoire, Auto-Immunity, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Hahn, M. J. Nicholson, J. Pyrdol, K. W. Wucherpfennig
Unconventional Topology Of Self Peptide-Major Histocompatibility Complex Binding By A Human Autoimmune T Cell Receptor.
Nat. Immunol. V. 6 490 2005
PubMed-ID: 15821740 | Reference-DOI: 10.1038/NI1187

Molecule 1 - HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DR ALPHA CHAIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	DROSOPHILA MELANOGASTER
	Expression System Common	:	FRUIT FLY
	Expression System Plasmid	:	PACDB3
	Expression System Strain	:	SF9
	Expression System Taxid	:	7227
	Expression System Vector Type	:	PLASMID
	Gene	:	HLA-DRA
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	HLA-DR2B ALPHA

Molecule 2 - HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DR BETA CHAIN
	Chains	:	B
	Engineered	:	YES
	Expression System	:	DROSOPHILA MELANOGASTER
	Expression System Common	:	FRUIT FLY
	Expression System Plasmid	:	PACDB3
	Expression System Strain	:	SF9
	Expression System Taxid	:	7227
	Expression System Vector Type	:	PLASMID
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	HLA-DR2B BETA

Molecule 3 - MBP PEPTIDE
	Chains	:	C
	Engineered	:	YES
	Synthetic	:	YES

Molecule 4 - T CELL RECEPTOR ALPHA CHAIN
	Chains	:	D
	Engineered	:	YES
	Expression System	:	DROSOPHILA MELANOGASTER
	Expression System Common	:	FRUIT FLY
	Expression System Plasmid	:	PACDB3
	Expression System Strain	:	SF9
	Expression System Taxid	:	7227
	Expression System Vector Type	:	PLASMID
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	TCR OB.1A12 ALPHA

Molecule 5 - T-CELL RECEPTOR BETA CHAIN
	Chains	:	E
	Engineered	:	YES
	Expression System	:	DROSOPHILA MELANOGASTER
	Expression System Common	:	FRUIT FLY
	Expression System Plasmid	:	PACDB3
	Expression System Strain	:	SF9
	Expression System Taxid	:	7227
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	TCR OB.1A12 BETA

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

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 1)

No.	Name	Count	Type	Full Name
1	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:118 , TRP A:168	BINDING SITE FOR RESIDUE NAG A 192

Asymmetric/Biological Unit

No.	Residues
1	A:107	-	A:163
2	B:15	-	B:79
3	B:117	-	B:173
4	D:23	-	D:89
5	E:23	-	E:94
6	E:149	-	E:214

Asymmetric/Biological Unit

No.	Residues
1	Asn A:15	-	Pro A:16
2	Thr A:113	-	Pro A:114
3	Tyr B:123	-	Pro B:124
4	Tyr E:155	-	Pro E:156

Asymmetric/Biological Unit (7, 7)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_050365	F	55	Y	2B1F_HUMAN	Polymorphism	16822516	B	F	26	Y
2	UniProt	VAR_038162	Y	59	H	2B1F_HUMAN	Polymorphism	11554462	B	Y	30	H
3	UniProt	VAR_038163	I	96	F	2B1F_HUMAN	Polymorphism	17886918	B	I	67	F
4	UniProt	VAR_050366	T	106	N	2B1F_HUMAN	Polymorphism	9269941	B	T	77	N
5	UniProt	VAR_038164	V	115	G	2B1F_HUMAN	Polymorphism	17885482	B	V	86	G
6	UniProt	VAR_050367	G	164	S	2B1F_HUMAN	Polymorphism	1059633	B	G	135	S
7	UniProt	VAR_050368	A	169	T	2B1F_HUMAN	Polymorphism	2308768	B	A	140	T

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

Asymmetric/Biological Unit (2, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IG_MHC	PS00290	Immunoglobulins and major histocompatibility complex proteins signature.	DRA_HUMAN	186-192	1	A:161-167
1	IG_MHC	PS00290		2B1F_HUMAN	200-206	1	B:171-177
2	MYELIN_MBP	PS00569	Myelin basic protein signature.	MBP_HUMAN	220-226	1	C:88-94

Asymmetric/Biological Unit (10, 10)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.2a	ENST00000355994	2a	ENSE00001421865	chr18:74844774-74844536	239	MBP_HUMAN	-	0	0	-	-
1.4	ENST00000355994	4	ENSE00002187900	chr18:74817242-74817167	76	MBP_HUMAN	1-17	17	0	-	-
1.8a	ENST00000355994	8a	ENSE00001400728	chr18:74778341-74778254	88	MBP_HUMAN	18-47	30	0	-	-
1.10e	ENST00000355994	10e	ENSE00001432843	chr18:74729224-74728788	437	MBP_HUMAN	47-192	146	0	-	-
1.13c	ENST00000355994	13c	ENSE00001179369	chr18:74702016-74701912	105	MBP_HUMAN	193-227	35	1	C:85-95	11
1.14e	ENST00000355994	14e	ENSE00001000086	chr18:74700868-74700833	36	MBP_HUMAN	228-239	12	1	C:96-98	3
1.14g	ENST00000355994	14g	ENSE00001278460	chr18:74700483-74700451	33	MBP_HUMAN	240-250	11	0	-	-
1.14o	ENST00000355994	14o	ENSE00001656901	chr18:74696850-74696731	120	MBP_HUMAN	251-290	40	0	-	-
1.15l	ENST00000355994	15l	ENSE00001606913	chr18:74692427-74690790	1638	MBP_HUMAN	291-304	14	0	-	-

2.3	ENST00000360004	3	ENSE00001930619	chr6:32557625-32557420	206	2B1F_HUMAN	1-34	34	1	B:3-5	3
2.4	ENST00000360004	4	ENSE00001731226	chr6:32552155-32551886	270	2B1F_HUMAN	34-124	91	1	B:5-95	91
2.5b	ENST00000360004	5b	ENSE00001801024	chr6:32549615-32549334	282	2B1F_HUMAN	124-218	95	1	B:95-189 (gaps)	95
2.6	ENST00000360004	6	ENSE00001717727	chr6:32548633-32548523	111	2B1F_HUMAN	218-255	38	1	B:189-189	1
2.7	ENST00000360004	7	ENSE00001773376	chr6:32548047-32548024	24	2B1F_HUMAN	255-263	9	0	-	-
2.8	ENST00000360004	8	ENSE00001954617	chr6:32546881-32546546	336	2B1F_HUMAN	263-266	4	0	-	-

3.6a	ENST00000383259	6a	ENSE00001839042	HSCHR6_MHC_QBL:32365090-32365280	191	DRA_HUMAN	1-28	28	1	A:2-3	2
3.7b	ENST00000383259	7b	ENSE00001719010	HSCHR6_MHC_QBL:32367694-32367939	246	DRA_HUMAN	28-110	83	1	A:3-85	83
3.8c	ENST00000383259	8c	ENSE00001737588	HSCHR6_MHC_QBL:32368431-32368712	282	DRA_HUMAN	110-204	95	1	A:85-179	95
3.9a	ENST00000383259	9a	ENSE00001770912	HSCHR6_MHC_QBL:32369002-32369167	166	DRA_HUMAN	204-254	51	1	A:179-183	5
3.10b	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:182
 aligned with DRA_HUMAN | P01903 from UniProtKB/Swiss-Prot  Length:254

    Alignment length:182
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206  
            DRA_HUMAN    27 KEEHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGALANIAVDKANLEIMTKRSNYTPITNVPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVTWLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCRVEHWGLDEPLLKHWEFDAP 208
               SCOP domains -----------d1ymma2 A:13-81 Class II MHC alpha chain, N-terminal domain          -d1ymma1 A:83-179 Class II MHC alpha chain, C-terminal domain                                     ---- SCOP domains
               CATH domains 1ymmA01 A:2-81                                                                  1ymmA02 A:82-183 Immunoglobulins                                                                       CATH domains
               Pfam domains --MHC_II_alpha-1ymmA02 A:4-84                                                      --------C1-set-1ymmA01 A:93-175                                                            -------- Pfam domains
         Sec.struct. author ....eeeeeeeeee...eeeeeeee..eeeeee.......ee.hhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.............eee.........eeeeeeeeee.....eeeeee..eee....ee...ee.....eeeeeeeee.......eeeeee.......eeeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC ---------------- PROSITE
           Transcript 3 (1) 3.---------------------------------------------------------------------------------Exon 3.8c  PDB: A:85-179 UniProt: 110-204                                                      ---- Transcript 3 (1)
           Transcript 3 (2) -Exon 3.7b  PDB: A:3-85 UniProt: 28-110                                             ---------------------------------------------------------------------------------------------3.9a  Transcript 3 (2)
                 1ymm A   2 KEEHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGALANIAVDKANLEIMTKRSNYTPITNVPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVTWLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCRVEHWGLDEPLLKHWEFDAP 183
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181

Chain B from PDB  Type:PROTEIN  Length:178
 aligned with 2B1F_HUMAN | P01911 from UniProtKB/Swiss-Prot  Length:266

    Alignment length:187
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       
           2B1F_HUMAN    32 TRPRFLWQPKRECHFFNGTERVRFLDRYFYNQEESVRFDSDVGEFRAVTELGRPDAEYWNSQKDILEQARAAVDTYCRHNYGVVESFTVQRRVQPKVTVYPSKTQPLQHHNLLVCSVSGFYPGSIEVRWFLNGQEEKAGMVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPSVTSPLTVEWR 218
               SCOP domains d1ymmb2 B:3-92 Class II MHC beta chain, N-terminal domain                                 d1ymmb1 B:93         -189 Class II MHC beta chain, C-terminal domain                              SCOP domains
               CATH domains 1ymmB01 B:3-91 Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1      1ymmB02 B:92-         189 Immunoglobulins                                                          CATH domains
               Pfam domains ----------MHC_II_beta-1ymmB02 B:13-87                                                ---------------C1         -set-1ymmB01 B:103-185                                                  ---- Pfam domains
         Sec.struct. author ....eee..eeeeeeehhhheee.eeeeee..eeeeeee......ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeee..---------.eeeeeeee.....eeeeee..eee...ee...........eeeeeee.........eeeeee.......eeeee. Sec.struct. author
                 SAPs(SNPs) -----------------------Y---H------------------------------------F---------N--------G------------------------------------------------S----T------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC ------------ PROSITE
           Transcript 2 (1) 2.3-----------------------------------------------------------------------------------------Exon 2.5b  PDB: B:95-189 (gaps) UniProt: 124-218                                                Transcript 2 (1)
           Transcript 2 (2) --Exon 2.4  PDB: B:5-95 UniProt: 34-124                                                      ---------------------------------------------------------------------------------------------2 Transcript 2 (2)
                 1ymm B   3 TRPRFLWQPKRECHFFNGTERVRFLDRYFYNQEESVRFDSDVGEFRAVTELGRPDAEYWNSQKDILEQARAAVDTYCRHNYGVVESFTVQRRVQPKVTVYPS---------LLVCSVSGFYPGSIEVRWFLNGQEEKAGMVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPSVTSPLTVEWR 189
                                    12        22        32        42        52        62        72        82        92       102 |       - |     122       132       142       152       162       172       182       
                                                                                                                               104       114

Chain C from PDB  Type:PROTEIN  Length:14
 aligned with MBP_HUMAN | P02686 from UniProtKB/Swiss-Prot  Length:304

    Alignment length:14
                                   226    
            MBP_HUMAN   217 ENPVVHFFKNIVTP 230
               SCOP domains -------------- SCOP domains
               CATH domains -------------- CATH domains
               Pfam domains Myelin_MBP-1ym Pfam domains
         Sec.struct. author .............. Sec.struct. author
                 SAPs(SNPs) -------------- SAPs(SNPs)
                    PROSITE ---MYELIN_---- PROSITE
               Transcript 1 Exon 1.13c 1.1 Transcript 1
                 1ymm C  85 ENPVVHFFKNIVTP  98
                                    94

Chain D from PDB  Type:PROTEIN  Length:96
                                                                                                                                
               SCOP domains d1ymmd1 D:9-104 T-cell antigen receptor                                                          SCOP domains
               CATH domains 1ymmD00 D:9-104 Immunoglobulins                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....................eeeeeee............eee...............hhhhh.................eeeeee......eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------ Transcript
                 1ymm D   9 QALSIQEGENATMNCSYKTSINNLQWYRQNSGRGLVHLILIRSNEREKHSGRLRVTLDTSKKSSSLLITASRAADTASYFCATDTTSGTYKYIFGT 104
                                    18        28        38        48        58        68        78        88        98

Chain E from PDB  Type:PROTEIN  Length:246
 aligned with TRBC1_HUMAN | P01850 from UniProtKB/Swiss-Prot  Length:177

    Alignment length:246
                                                                                                                                                  1                                                                                                                               
                                     -         -         -         -         -         -         -         -         -         -         -        |2        12        22        32        42        52        62        72        82        92       102       112       122      
          TRBC1_HUMAN     - ----------------------------------------------------------------------------------------------------------------------EDLNKVFPPEVAVFEPSEAEISHTQKATLVCLATGFFPDHVELSWWVNGKEVHSGVSTDPQPLKEQPALNDSRYCLSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGR 128
               SCOP domains d1ymme1 E:1-119 T-cell antigen receptor                                                                                ---d1ymme2 E:123-246 T-cell antigen receptor                                                                                    SCOP domains
               CATH domains --1ymmE01 E:3-119 Immunoglobulins                                                                                      1ymmE02 E:120-246 Immunoglobulins                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------C1-set-1ymmE01 E:133-226                                                                      -------------------- Pfam domains
         Sec.struct. author ...eee...eee.......ee.eee......eeeeeee.......eeeeee......ee...................ee..........eeeee..................eee...hhhhh...ee.......hhhhhh...eeeeeee..........ee..............................eeeee............eeeeee....................eeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1ymm E   1 GAVVSQHPSWVISKSGTSVKIECRSLDFQATTMFWYRQFPKQSLMLMATSNEGSKATYEQGVEKDKFLINHASLTLSTLTVTSAHPEDSSFYICSARDLTSGANNEQFFGPGTRLTVLEDLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVSTDPQPLKEQPALNDSRYSLSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGR 246
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Roll (3276)

Topology: Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 (75)

Homologous Superfamily: Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 (75)

Human (Homo sapiens) (48)

1a	1ymmB01	B:3-91
1b	1ymmA01	A:2-81

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Immunoglobulins (2282)

Human (Homo sapiens) (912)

2a	1ymmD00	D:9-104
2b	1ymmA02	A:82-183
2c	1ymmE02	E:120-246
2d	1ymmB02	B:92-189
2e	1ymmE01	E:3-119

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Ig (577)

Family: C1-set (338)

Homo sapiens (Human) (218)

1a	C1-set-1ymmB01	B:103-185
1b	C1-set-1ymmA01	A:93-175
1c	C1-set-1ymmE01	E:133-226

Clan: MHC (252)

Family: MHC_II_alpha (42)

Homo sapiens (Human) (26)

MHC_II_alpha-1ymmA02

A:4-84

Family: MHC_II_beta (39)

Homo sapiens (Human) (25)

MHC_II_beta-1ymmB02

B:13-87

Clan: no clan defined [family: Myelin_MBP] (2)

Family: Myelin_MBP (2)

Homo sapiens (Human) (2)

Myelin_MBP-1ymmC01

C:85-98

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (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 B (2B1F_HUMAN | P01911)

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.
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: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: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.
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: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 C (MBP_HUMAN | P02686)

molecular function
	GO:0002020	protease binding	Interacting selectively and non-covalently with any protease or peptidase.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0019911	structural constituent of myelin sheath	The action of a molecule that contributes to the structural integrity of the myelin sheath of a nerve.
biological process
	GO:0007568	aging	A developmental process that is a deterioration and loss of function over time. Aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Aging includes cellular senescence, but is more inclusive. May precede death and may succeed developmental maturation (GO:0021700).
	GO:0008366	axon ensheathment	Any process in which the axon of a neuron is insulated, and that insulation maintained, thereby preventing dispersion of the electrical signal.
	GO:0007417	central nervous system development	The process whose specific outcome is the progression of the central nervous system over time, from its formation to the mature structure. The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the brain and spinal cord. In those invertebrates with a central nervous system it typically consists of a brain, cerebral ganglia and a nerve cord.
	GO:0007268	chemical synaptic transmission	The vesicular release of classical neurotransmitter molecules from a presynapse, across a chemical synapse, the subsequent activation of neurotransmitter receptors at the postsynapse of a target cell (neuron, muscle, or secretory cell) and the effects of this activation on the postsynaptic membrane potential and ionic composition of the postsynaptic cytosol. This process encompasses both spontaneous and evoked release of neurotransmitter and all parts of synaptic vesicle exocytosis. Evoked transmission starts with the arrival of an action potential at the presynapse.
	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:0061024	membrane organization	A process which results in the assembly, arrangement of constituent parts, or disassembly of a membrane. A membrane is a double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins.
	GO:0042552	myelination	The process in which myelin sheaths are formed and maintained around neurons. Oligodendrocytes in the brain and spinal cord and Schwann cells in the peripheral nervous system wrap axons with compact layers of their plasma membrane. Adjacent myelin segments are separated by a non-myelinated stretch of axon called a node of Ranvier.
	GO:0050771	negative regulation of axonogenesis	Any process that stops, prevents, or reduces the frequency, rate or extent of axonogenesis.
	GO:0070542	response to fatty acid	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a fatty acid stimulus.
	GO:0046689	response to mercury ion	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a mercury ion stimulus.
	GO:0032570	response to progesterone	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a progesterone stimulus.
	GO:0009636	response to toxic substance	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a toxic stimulus.
	GO:0034612	response to tumor necrosis factor	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a tumor necrosis factor stimulus.
	GO:0021762	substantia nigra development	The progression of the substantia nigra over time from its initial formation until its mature state. The substantia nigra is the layer of gray substance that separates the posterior parts of the cerebral peduncles (tegmentum mesencephali) from the anterior parts; it normally includes a posterior compact part with many pigmented cells (pars compacta) and an anterior reticular part whose cells contain little pigment (pars reticularis).
cellular component
	GO:0071944	cell periphery	The part of a cell encompassing the cell cortex, the plasma membrane, and any external encapsulating structures.
	GO:0042995	cell projection	A prolongation or process extending from a cell, e.g. a flagellum or axon.
	GO:0043218	compact myelin	The portion of the myelin sheath in which layers of cell membrane are tightly juxtaposed, completely excluding cytoplasm. The juxtaposed cytoplasmic surfaces form the major dense line, while the juxtaposed extracellular surfaces form the interperiod line visible in electron micrographs.
	GO:0033269	internode region of axon	An axon part that is located between the nodes of Ranvier and surrounded by compact myelin sheath.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0043209	myelin sheath	An electrically insulating fatty layer that surrounds the axons of many neurons. It is an outgrowth of glial cells: Schwann cells supply the myelin for peripheral neurons while oligodendrocytes supply it to those of the central nervous system.
	GO:0043025	neuronal cell body	The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
	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 E (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.

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(no "Related Entries Specified in the PDB File" available for 1YMM)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (6, 6)

Cis Peptide Bonds (4, 4)

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Exons (10, 10)

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