1JCK - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   T-CELL RECEPTOR BETA CHAIN COMPLEXED WITH SEC3 SUPERANTIGEN

Authors :   B. A. Fields, R. A. Mariuzza

Date :   22 Oct 96 (Deposition) - 12 Nov 97 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.50

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

Keywords :   T-Cell, Receptor, Transmembrane, Glycoprotein, Signal, Enterotoxin, Toxin, Superantigen, Complex (Toxin/Receptor) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. A. Fields, E. L. Malchiodi, H. Li, X. Ysern, C. V. Stauffacher, P. M. Schlievert, K. Karjalainen, R. A. Mariuzza
Crystal Structure Of A T-Cell Receptor Beta-Chain Complexed With A Superantigen.
Nature V. 384 188 1996
PubMed-ID: 8906797 | Reference-DOI: 10.1038/384188A0
(for further references see the PDB file header)

Molecule 1 - 14.3.D T CELL ANTIGEN RECEPTOR
	Chains	:	A, C
	Engineered	:	YES
	Expression System	:	MUS MUSCULUS
	Expression System Common	:	HOUSE MOUSE
	Expression System Taxid	:	10090
	Fragment	:	BETA CHAIN
	Mutation	:	YES
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

Molecule 2 - STAPHYLOCOCCAL ENTEROTOXIN C3
	Chains	:	B, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	STAPHYLOCOCCUS AUREUS
	Organism Taxid	:	1280
	Strain	:	FRI913
	Synonym	:	SEC3

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

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1JCK)

(no "Site" information available for 1JCK)

Asymmetric/Biological Unit

No.	Residues
1	A:23	-	A:92
2	A:147	-	A:212
3	B:93	-	B:110
4	C:23	-	C:92
5	C:147	-	C:212
6	D:93	-	D:110

Asymmetric/Biological Unit

No.	Residues
1	Ser A:7	-	Pro A:8
2	Phe A:153	-	Pro A:154
3	Ser C:7	-	Pro C:8
4	Phe C:153	-	Pro C:154

(no "SAP(SNP)/Variant" information available for 1JCK)

Asymmetric/Biological Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	STAPH_STREP_TOXIN_1	PS00277	Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin signature 1.	ENTC3_STAAU	139-148	2	B:112-121 D:112-121
2	STAPH_STREP_TOXIN_2	PS00278	Staphyloccocal enterotoxin/Streptococcal pyrogenic exotoxin signature 2.	ENTC3_STAAU	178-201	2	B:151-174 D:151-174

(no "Exon" information available for 1JCK)

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:238
                                                                                                                                                                                                                                                                               
               SCOP domains d1jcka1 A:3-117 T-cell antigen receptor                                                                          d1jcka2 A:118-246 T-cell antigen receptor                                                                                     SCOP domains
               CATH domains 1jckA01 A:3-117 Immunoglobulins                                                                                  1jckA02 A:118-246 Immunoglobulins                                                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
     Sec.struct. author (1) ..eee..eeeee....eeeeee......eeeeeee.....eeeeeee..............eeee.....eeeeee....hhh.eeeeeeee.....hhheee...eeeeee..hhh....eeeee...hhh........eeeeeeee....------hhh.............eeee..eeeeeeee...hhhh.....eeeeeeee...................eeeeeee.... Sec.struct. author (1)
     Sec.struct. author (2) --------------------------------------------------------------------------------------------------------------------------------------------------------eeeeeee------------------------------------------------------------------------------- Sec.struct. author (2)
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1jck A    3 AVTQSPRNKVAVTGGKVTLSCQQTNNHNNMYWYRQDTGHGLRLIHYSYGAGSTEKGDIPDGYKASRPSQEQFSLILELATPSQTSVYFCASGGGRGSYAEQFFGPGTRLTVLEDLRQVTPPKVSLFEPSKAEIANKQKATLVCLARGFFPDHVELSWWVNGKEVHSGVSTDPQAYKESNYSYCLSSRLRVSATFWHNPRNHFRCQVQFHGLSEEDKWPEGSPKPVTQNISAEAWGRAD  246
                                    12        22        32        42        52        62||      73        83        93       105       115 |     124       134       144       154       164       174       187|      198       208       218       228       238        
                                                                                       63|                                  102|        116A                                                               182|||                                                         
                                                                                        65                                   105                                                                            186||                                                         
                                                                                                                                                                                                             187|                                                         
                                                                                                                                                                                                              189

Chain B from PDB  Type:PROTEIN  Length:239
 aligned with ENTC3_STAAU | P0A0L5 from UniProtKB/Swiss-Prot  Length:266

    Alignment length:239
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257         
         ENTC3_STAAU     28 ESQPDPMPDDLHKSSEFTGTMGNMKYLYDDHYVSATKVKSVDKFLAHDLIYNISDKKLKNYDKVKTELLNEDLAKKYKDEVVDVYGSNYYVNCYFSSKDNVGKVTGGKTCMYGGITKHEGNHFDNGNLQNVLVRVYENKRNTISFEVQTDKKSVTAQELDIKARNFLINKKNLYEFNSSPYETGYIKFIENNGNTFWYDMMPAPGDKFDQSKYLMMYNDNKTVDSKSVKIEVHLTTKNG  266
               SCOP domains d1jckb1 B:1-121 Staphylococcal enterotoxin C3, SEC3                                                                      d1jckb2 B:122-239 Staphylococcal enterotoxin C3, SEC3                                                                  SCOP domains
               CATH domains 1jckB02 B:1-31,B:120-237       1jckB01 B:32-119  [code=2.40.50.110, no name defined]                                   1jckB02 B:1-31,B:120-237  [code=3.10.20.120, no name defined]                                                         -- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhh....hhhhhhhh....eeeeee.eeee....eeeee........eeeeeee...hhhhhhh....eeeee....................eeeeee..eee.............eeeeeee...eeeeeee.....eeehhhhhhhhhhhhhhh............eeeeeee.....eeeee..........hhhhhhhh....eee....eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------STAPH_STRE-----------------------------STAPH_STREP_TOXIN_2     ----------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1jck B    1 ESQPDPMPDDLHKSSEFTGTMGNMKYLYDDHYVSATKVKSVDKFLAHDLIYNINDKKLNNYDKVKTELLNEDLANKYKDEVVDVYGSNYYVNCYFSSKDNVGKVTSGKTCMYGGITKHEGNHFDNGNLQNVLIRVYENKRNTISFEVQTDKKSVTAQELDIKARNFLINKKNLYEFNSSPYETGYIKFIESNGNTFWYDMMPAPGDKFDQSKYLMIYKDNKMVDSKSVKIEVHLTTKNG  239
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230

Chain C from PDB  Type:PROTEIN  Length:238
                                                                                                                                                                                                                                                                               
               SCOP domains d1jckc1 C:3-117 T-cell antigen receptor                                                                          d1jckc2 C:118-246 T-cell antigen receptor                                                                                     SCOP domains
               CATH domains 1jckC01 C:3-117 Immunoglobulins                                                                                  1jckC02 C:118-246 Immunoglobulins                                                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
     Sec.struct. author (1) ..eee..eeeee....eeeeee......eeeeeee.....eeeeeee..............eeee.....eeeeee....hhh.eeeeeeee.....hhheee...eeeeee..hhh....eeeee...hhh........eeeeeeee....------hhh.............eeee..eeeeeeee...hhhh.....eeeeeeee...................eeeeeee.... Sec.struct. author (1)
     Sec.struct. author (2) --------------------------------------------------------------------------------------------------------------------------------------------------------eeeeeee------------------------------------------------------------------------------- Sec.struct. author (2)
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1jck C    3 AVTQSPRNKVAVTGGKVTLSCQQTNNHNNMYWYRQDTGHGLRLIHYSYGAGSTEKGDIPDGYKASRPSQEQFSLILELATPSQTSVYFCASGGGRGSYAEQFFGPGTRLTVLEDLRQVTPPKVSLFEPSKAEIANKQKATLVCLARGFFPDHVELSWWVNGKEVHSGVSTDPQAYKESNYSYCLSSRLRVSATFWHNPRNHFRCQVQFHGLSEEDKWPEGSPKPVTQNISAEAWGRAD  246
                                    12        22        32        42        52        62||      73        83        93       105       115 |     124       134       144       154       164       174       187|      198       208       218       228       238        
                                                                                       63|                                  102|        116A                                                               182|||                                                         
                                                                                        65                                   105                                                                            186||                                                         
                                                                                                                                                                                                             187|                                                         
                                                                                                                                                                                                              189

Chain D from PDB  Type:PROTEIN  Length:239
 aligned with ENTC3_STAAU | P0A0L5 from UniProtKB/Swiss-Prot  Length:266

    Alignment length:239
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257         
         ENTC3_STAAU     28 ESQPDPMPDDLHKSSEFTGTMGNMKYLYDDHYVSATKVKSVDKFLAHDLIYNISDKKLKNYDKVKTELLNEDLAKKYKDEVVDVYGSNYYVNCYFSSKDNVGKVTGGKTCMYGGITKHEGNHFDNGNLQNVLVRVYENKRNTISFEVQTDKKSVTAQELDIKARNFLINKKNLYEFNSSPYETGYIKFIENNGNTFWYDMMPAPGDKFDQSKYLMMYNDNKTVDSKSVKIEVHLTTKNG  266
               SCOP domains d1jckd1 D:1-121 Staphylococcal enterotoxin C3, SEC3                                                                      d1jckd2 D:122-239 Staphylococcal enterotoxin C3, SEC3                                                                  SCOP domains
               CATH domains 1jckD02 D:1-31,D:120-237       1jckD01 D:32-119  [code=2.40.50.110, no name defined]                                   1jckD02 D:1-31,D:120-237  [code=3.10.20.120, no name defined]                                                         -- CATH domains
           Pfam domains (1) ----------------------Stap_Strp_toxin-1jckD03 D:23-118                                                                ----------Stap_Strp_tox_C-1jckD01 D:129-235                                                                          ---- Pfam domains (1)
           Pfam domains (2) ----------------------Stap_Strp_toxin-1jckD04 D:23-118                                                                ----------Stap_Strp_tox_C-1jckD02 D:129-235                                                                          ---- Pfam domains (2)
         Sec.struct. author .............hhh....hhhhhhhh....eeeeee.eeee....eeeee........eeeeeee...hhhhhhh....eeeee....................eeeeee..eee.............eeeeeee...eeeeeee.....eeehhhhhhhhhhhhhhh............eeeeeee.....eeeee..........hhhhhhhh....eee....eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------STAPH_STRE-----------------------------STAPH_STREP_TOXIN_2     ----------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1jck D    1 ESQPDPMPDDLHKSSEFTGTMGNMKYLYDDHYVSATKVKSVDKFLAHDLIYNINDKKLNNYDKVKTELLNEDLANKYKDEVVDVYGSNYYVNCYFSSKDNVGKVTSGKTCMYGGITKHEGNHFDNGNLQNVLIRVYENKRNTISFEVQTDKKSVTAQELDIKARNFLINKKNLYEFNSSPYETGYIKFIESNGNTFWYDMMPAPGDKFDQSKYLMIYKDNKMVDSKSVKIEVHLTTKNG  239
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230

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: Ubiquitin-like (UB roll) (674)

Homologous Superfamily: [code=3.10.20.120, no name defined] (91)

House mouse (Mus musculus) (7)

1a	1jckB02	B:1-31,B:120-237
1b	1jckD02	D:1-31,D:120-237

Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: OB fold (Dihydrolipoamide Acetyltransferase, E2P) (1040)

Homologous Superfamily: [code=2.40.50.110, no name defined] (136)

House mouse (Mus musculus) (7)

2a	1jckB01	B:32-119
2b	1jckD01	D:32-119

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Immunoglobulins (2282)

House mouse (Mus musculus) (616)

3a	1jckA01	A:3-117
3b	1jckC01	C:3-117
3c	1jckA02	A:118-246
3d	1jckC02	C:118-246

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Ant-toxin_C (48)

Family: Stap_Strp_tox_C (48)

Staphylococcus aureus (41)

1a	Stap_Strp_tox_C-1jckD01	D:129-235
1b	Stap_Strp_tox_C-1jckD02	D:129-235

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

Family: Stap_Strp_toxin (39)

Staphylococcus aureus (33)

2a	Stap_Strp_toxin-1jckD03	D:23-118
2b	Stap_Strp_toxin-1jckD04	D:23-118

Asymmetric/Biological Unit(hide GO term definitions)

Chain B,D (ENTC3_STAAU | P0A0L5)

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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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Phe A:153 - Pro A:154	[ RasMol ]
		Phe C:153 - Pro C:154	[ RasMol ]
		Ser A:7 - Pro A:8	[ RasMol ]
		Ser C:7 - Pro C:8	[ RasMol ]

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	1jck
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Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (6, 6)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Exons (0, 0)

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