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Asym./Biol. Unit (Jmol Viewer)

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Title :   CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN HUMAN T CELL RECEPTOR AND STAPHYLOCOCCAL ENTEROTOXIN

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) - 24 Aug 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Immune System, Superantigen (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

		1	2	3
Asymmetric/Biological Unit	:	A	B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 4)

No.	Name	Count	Type	Full Name
1	GOL	3	Ligand/Ion	GLYCEROL
2	NA	1	Ligand/Ion	SODIUM ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	MET A:162 , VAL B:196 , SER B:197	BINDING SITE FOR RESIDUE GOL B1244
2	AC2	SOFTWARE	VAL B:155 , GLU B:156 , LEU B:157	BINDING SITE FOR RESIDUE GOL B1245
3	AC3	SOFTWARE	TRP B:223 , GLN B:225 , ASP B:226 , ARG B:227 , ALA B:228	BINDING SITE FOR RESIDUE GOL B1246
4	AC4	SOFTWARE	HOH A:2023 , HIS C:23 , SER C:77 , HOH C:2016 , HOH C:2038	BINDING SITE FOR RESIDUE NA C1216

Asymmetric/Biological Unit

No.	Residues
1	A:23	-	A:89
2	A:158	-	B:171
3	B:25	-	B:93
4	B:145	-	B:210
5	C:82	-	C:92

Asymmetric/Biological Unit

No.	Residues
1	Ser A:7	-	Pro A:8
2	Ser A:127	-	Ser A:128
3	Ser A:128	-	Asp A:129
4	Ser B:9	-	Pro B:10
5	Tyr B:151	-	Pro B:152
6	Lys C:214	-	Lys C:215

(no "SAP(SNP)/Variant" information available for 2XNA)

Asymmetric/Biological Unit (1, 1)

	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

(no "Exon" information available for 2XNA)

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 d2xnaa1 A:2-111 automated matches                                                                             d2xnaa2 A:112-200 automated matches                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------DUF1968-2xnaA01 A:117-200                                                            Pfam domains
         Sec.struct. author ...eee..eeeee....eeeeee.......eeeeee......eeeeee.....eeee..eeeee.....eeeeee...hhhhheeeeeeee.....eee...eeeeee........eeeeee.......eeeeee................ee...eeeeehhhheeeeeeeee......hhhhhh............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xna 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:241
 aligned with TRBC1_HUMAN | P01850 from UniProtKB/Swiss-Prot  Length:177

    Alignment length:241
                                                                                                                                            1                                                                                                                                
                                     -         -         -         -         -         -         -         -         -         -         -  |      8        18        28        38        48        58        68        78        88        98       108       118       128 
          TRBC1_HUMAN     - ----------------------------------------------------------------------------------------------------------------EDLNKVFPPEVAVFEPSEAEISHTQKATLVCLATGFFPDHVELSWWVNGKEVHSGVSTDPQPLKEQPALNDSRYCLSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRA 129
               SCOP domains d2xnab1 B:3-115 automated matches                                                                                d2xnab2 B:116-243 automated matches                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------C1-set-2xnaB01 B:129-222                                                                      --------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee.....eeeeeeee...eeeeeeeeee..eeee......eee.........eee........eeeeeeee.......ee...eeeeee.hhhhh...eeeee..hhhhhhhhheeeeeeeeeee....eeeeeee..eee...eee....ee.........eeeeeeeeeehhhhh....eeeeeeee..................eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xna B   3 DGGITQSPKYLFRKEGQNVTLSCEQNLNHDAMYWYRQDPGQGLRLIYYSQIVNDFQKGDIAEGYSVSREKKESFPLTVTSAQKNPTAFYLCASSSRSSYEQYFGPGTRLTVTEDLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALNDSRYSLSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRA 243
                                    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 d2xnac1 C:1-101 Staphylococcal enterotoxin H, SEH                                                    d2xnac2 C:102-215 Staphylococcal enterotoxin H, SEH                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------Stap_Strp_toxin-2xnaC02 C:13-100                                                        -------Stap_Strp_tox_C-2xnaC01 C:108-212                                                                        --- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhh.eeeeee....ee...eeee...hhhhheeeee..hhhhhhhhh...eeeee..............eeeee..eee...eeeeeeeeeeeeee..ee...eeeeeee.eeehhhhhhhhhhhhhhhhh.......eeeeeeeeee.....eeee.......hhhhhhhhhh...eee...eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------STAPH_STREP_TOXIN_2     -------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xna 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

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 "CATH Domain" information available for 2XNA)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Ant-toxin_C (48)

Family: Stap_Strp_tox_C (48)

Staphylococcus aureus (41)

Stap_Strp_tox_C-2xnaC01

C:108-212

Clan: Ig (577)

Family: C1-set (338)

Homo sapiens (Human) (218)

C1-set-2xnaB01

B:129-222

Clan: no clan defined [family: DUF1968] (16)

Family: DUF1968 (16)

Homo sapiens (Human) (14)

DUF1968-2xnaA01

A:117-200

Clan: no clan defined [family: Stap_Strp_toxin] (39)

Family: Stap_Strp_toxin (39)

Staphylococcus aureus (33)

Stap_Strp_toxin-2xnaC02

C:13-100

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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Lys C:214 - Lys C:215	[ RasMol ]
		Ser A:127 - Ser A:128	[ RasMol ]
		Ser A:128 - Asp A:129	[ RasMol ]
		Ser A:7 - Pro A:8	[ RasMol ]
		Ser B:9 - Pro B:10	[ RasMol ]
		Tyr B:151 - Pro B:152	[ RasMol ]

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1ewc	CRYSTAL STRUCTURE OF ZN2+ LOADED STAPHYLOCOCCAL ENTEROTOXIN H
1f77	STAPHYLOCOCCAL ENTEROTOXIN H DETERMINED TO 2. 4 A RESOLUTION
1fyt	CRYSTAL STRUCTURE OF A COMPLEX OF A HUMAN ALPHA/BETA-T CELLRECEPTOR, INFLUENZA HA ANTIGEN PEPTIDE, AND MHC CLASS IIMOLECULE, HLA-DR1
1j8h	CRYSTAL STRUCTURE OF A COMPLEX OF A HUMAN ALPHA/BETA-T CELLRECEPTOR, INFLUENZA HA ANTIGEN PEPTIDE, AND MHC CLASS IIMOLECULE, HLA-DR4
1kgc	IMMUNE RECEPTOR
1ktk	COMPLEX OF STREPTOCOCCAL PYROGENIC ENTEROTOXIN C (SPEC)WITH A HUMAN T CELL RECEPTOR BETA CHAIN (VBETA2.1)
1mi5	THE CRYSTAL STRUCTURE OF LC13 TCR IN COMPLEX WITH HLAB8- EBVPEPTIDE COMPLEX
1oga	A STRUCTURAL BASIS FOR IMMUNODOMINANT HUMAN T-CELL RECEPTOR RECOGNITION.
1qrn	CRYSTAL STRUCTURE OF HUMAN A6 TCR COMPLEXED WITH HLA-A2 BOUND TO ALTERED HTLV-1 TAX PEPTIDE P6A
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
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2eyt	A STRUCTURAL BASIS FOR SELECTION AND CROSS- SPECIESREACTIVITY OF THE SEMI-INVARIANT NKT CELL RECEPTOR INCD1D/GLYCOLIPID RECOGNITION
2gj6	THE COMPLEX BETWEEN TCR A6 AND HUMAN CLASS I MHC HLA-A2WITH THE MODIFIED HTLV-1 TAX (Y5K-4-[3-INDOLYL]-BUTYRICACID) PEPTIDE
2xn9	CRYSTAL STRUCTURE OF THE TERNARY COMPLEX BETWEEN HUMAN T CELL RECEPTOR, STAPHYLOCOCCAL ENTEROTOXIN H AND HUMAN MAJOR HISTOCOMPATIBILITY COMPLEX CLASS II

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (5, 5)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (4, 6)

CATH Domains (0, 0)

Pfam Domains (4, 4)

Gene Ontology (10, 16)

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