1TY2 - JenaLib

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Title :   CRYSTAL STRUCTURE OF THE STREPTOCOCCAL PYROGENIC EXOTOXIN J (SPE-J)

Authors :   H. M. Baker, T. Proft, P. D. Webb, V. L. Arcus, J. D. Fraser, E. N. Baker

Date :   07 Jul 04 (Deposition) - 17 Aug 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym. Unit : A,B,C
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C  (2x)

Keywords :   Superantigen, T-Cell Receptor Binding, Mutagenesis, Dimerization, Crystal Structure, Zinc Binding, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. M. Baker, T. Proft, P. D. Webb, V. L. Arcus, J. D. Fraser, E. N. Baker
Crystallographic And Mutational Data Show That The Streptococcal Pyrogenic Exotoxin J Can Use A Common Binding Surface For T-Cell Receptor Binding And Dimerization
J. Biol. Chem. V. 279 38571 2004
PubMed-ID: 15247241 | Reference-DOI: 10.1074/JBC.M406695200
(for further references see the PDB file header)

Molecule 1 - PUTATIVE EXOTOXIN (SUPERANTIGEN)
	Chains	:	A, B, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX-3C
	Expression System Strain	:	DH5A
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	SPE-J
	Organism Scientific	:	STREPTOCOCCUS PYOGENES
	Organism Taxid	:	1314
	Synonym	:	EXOTOXIN J, SPE-J

		1	2	3
Asymmetric Unit	:	A	B	C
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (2x)	:			C

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 3)

No.	Name	Count	Type	Full Name
1	ZN	3	Ligand/Ion	ZINC ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:169 , HIS A:203 , ASP A:205 , HOH A:735	BINDING SITE FOR RESIDUE ZN A 700
2	AC2	SOFTWARE	HIS B:169 , HIS B:203 , ASP B:205 , SER C:58 , HOH C:715	BINDING SITE FOR RESIDUE ZN B 701
3	AC3	SOFTWARE	HIS C:169 , HIS C:203 , ASP C:205 , HOH C:716	BINDING SITE FOR RESIDUE ZN C 702

(no "SS Bond" information available for 1TY2)

(no "Cis Peptide Bond" information available for 1TY2)

(no "SAP(SNP)/Variant" information available for 1TY2)

(no "PROSITE Motif" information available for 1TY2)

(no "Exon" information available for 1TY2)

Asymmetric 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:211
 aligned with Q7BAE3_STRPY | Q7BAE3 from UniProtKB/TrEMBL  Length:232

    Alignment length:211
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231 
         Q7BAE3_STRPY    22 KSDSENIKDVKLQLNYAYEIIPVDYTNCNIDYLTTHDFYIDISSYKKKNFSVDSEVESYITTKFTKNQKVNIFGLPYIFTRYDVYYIYGGVTPSVNSNSENSKIVGNLLIDGVQQKTLINPIKIDKPIFTIQEFDFKIRQYLMQTYKIYDPNSPYIKGQLEIAINGNKHESFNLYDATSSSTRSDIFKKYKDNKTINMKDFSHFDIYLWTK 232
               SCOP domains ---d1ty2a1 A:4-99 Streptococcal pyrogenic exotoxin Spe-J                                           ----d1ty2a2 A:104-211 Streptococcal pyrogenic exotoxin Spe-J                                                     SCOP domains
               CATH domains 1ty2A01             1ty2A02 A:21-95  [code=2.40.50.110, no name defined]                       1ty2A01 A:1-20,A:96-211  [code=3.10.20.120, no name defined]                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhh...eeeeeeeeeee...eeeeehhhhhh...eeeee....hhhhh....eeeeee.........eeeee..eee...........eeeeee..eeeeeee........eeehhhhhhhhhhhhhhhhh.........eeeeeeee...eeeeee........hhhhhhhhhhhh.eee...eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ty2 A   1 KSDSENIKDVKLQLNYAYEIIPVDYTNCNIDYLTTHDFYIDISSYKKKNFSVDSEVESYITTKFTKNQKVNIFGLPYIFTRYDVYYIYGGVTPSVNSNSENSKIVGNLLIDGVQQKTLINPIKIDKPIFTIQEFDFKIRQYLMQTYKIYDPNSPYIKGQLEIAINGNKHESFNLYDATSSSTRSDIFKKYKDNKTINMKDFSHFDIYLWTK 211
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

Chain B from PDB  Type:PROTEIN  Length:207
 aligned with Q7BAE3_STRPY | Q7BAE3 from UniProtKB/TrEMBL  Length:232

    Alignment length:211
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231 
         Q7BAE3_STRPY    22 KSDSENIKDVKLQLNYAYEIIPVDYTNCNIDYLTTHDFYIDISSYKKKNFSVDSEVESYITTKFTKNQKVNIFGLPYIFTRYDVYYIYGGVTPSVNSNSENSKIVGNLLIDGVQQKTLINPIKIDKPIFTIQEFDFKIRQYLMQTYKIYDPNSPYIKGQLEIAINGNKHESFNLYDATSSSTRSDIFKKYKDNKTINMKDFSHFDIYLWTK 232
               SCOP domains ---d1ty2b1 B:4-98 Streptococcal pyrogenic exotoxin Spe-J                                          -----d1ty2b2 B:104-211 Streptococcal pyrogenic exotoxin Spe-J                                                     SCOP domains
               CATH domains 1ty2B01             1ty2B02 B:21-95  [code=2.40.50.110, no name defined]                       1ty    2B01 B:1-20,B:96-211  [code=3.10.20.120, no name defined]                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhh...eeeeeeeeeee...eeeeehhhhhh...eeeee....hhhhh....eeeeee.........eeeee..eee.....----...eeeee..eeeeeee........eeehhhhhhhhhhhhhhhhh.........eeeeeeee.....eeee........hhhhhhhhhhhh.eee...eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ty2 B   1 KSDSENIKDVKLQLNYAYEIIPVDYTNCNIDYLTTHDFYIDISSYKKKNFSVDSEVESYITTKFTKNQKVNIFGLPYIFTRYDVYYIYGGVTPSVNSN----KIVGNLLIDGVQQKTLINPIKIDKPIFTIQEFDFKIRQYLMQTYKIYDPNSPYIKGQLEIAINGNKHESFNLYDATSSSTRSDIFKKYKDNKTINMKDFSHFDIYLWTK 211
                                    10        20        30        40        50        60        70        80        90       | -  |    110       120       130       140       150       160       170       180       190       200       210 
                                                                                                                            98  103

Chain C from PDB  Type:PROTEIN  Length:208
 aligned with Q7BAE3_STRPY | Q7BAE3 from UniProtKB/TrEMBL  Length:232

    Alignment length:208
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224        
         Q7BAE3_STRPY    25 SENIKDVKLQLNYAYEIIPVDYTNCNIDYLTTHDFYIDISSYKKKNFSVDSEVESYITTKFTKNQKVNIFGLPYIFTRYDVYYIYGGVTPSVNSNSENSKIVGNLLIDGVQQKTLINPIKIDKPIFTIQEFDFKIRQYLMQTYKIYDPNSPYIKGQLEIAINGNKHESFNLYDATSSSTRSDIFKKYKDNKTINMKDFSHFDIYLWTK 232
               SCOP domains d1ty2c1 C:4-99 Streptococcal pyrogenic exotoxin Spe-J                                           ----d1ty2c2 C:104-211 Streptococcal pyrogenic exotoxin Spe-J                                                     SCOP domains
               CATH domains 1ty2C01          1ty2C02 C:21-95  [code=2.40.50.110, no name defined]                       1ty2C01 C:4-20,C:96-211  [code=3.10.20.120, no name defined]                                                         CATH domains
           Pfam domains (1) -----------Stap_Strp_toxin-1ty2C04 C:15-94                                                 -------Stap_Strp_tox_C-1ty2C01 C:102-209                                                                           -- Pfam domains (1)
           Pfam domains (2) -----------Stap_Strp_toxin-1ty2C05 C:15-94                                                 -------Stap_Strp_tox_C-1ty2C02 C:102-209                                                                           -- Pfam domains (2)
           Pfam domains (3) -----------Stap_Strp_toxin-1ty2C06 C:15-94                                                 -------Stap_Strp_tox_C-1ty2C03 C:102-209                                                                           -- Pfam domains (3)
         Sec.struct. author ...hhhhhhhhhhhh....eeeeeeeeeee...eeeeehhhhhh...eeeee.hhhhhh......eeeeee.........eeeee..eee...........eeeeee..eeeeeee........eeehhhhhhhhhhhhhhhhh.........eeeeeeee...eeeeee........hhhhhhhhhhhh.eee...eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ty2 C   4 SENIKDVKLQLNYAYEIIPVDYTNCNIDYLTTHDFYIDISSYKKKNFSVDSEVESYITTKFTKNQKVNIFGLPYIFTRYDVYYIYGGVTPSVNSNSENSKIVGNLLIDGVQQKTLINPIKIDKPIFTIQEFDFKIRQYLMQTYKIYDPNSPYIKGQLEIAINGNKHESFNLYDATSSSTRSDIFKKYKDNKTINMKDFSHFDIYLWTK 211
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203

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 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)

Streptococcus pyogenes. Organism_taxid: 1314. (2)

1a	1ty2C01	C:4-20,C:96-211
1b	1ty2A01	A:1-20,A:96-211
1c	1ty2B01	B:1-20,B:96-211

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)

Streptococcus pyogenes. Organism_taxid: 1314. (2)

2a	1ty2A02	A:21-95
2b	1ty2B02	B:21-95
2c	1ty2C02	C:21-95

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Ant-toxin_C (48)

Family: Stap_Strp_tox_C (48)

Streptococcus pyogenes (4)

1a	Stap_Strp_tox_C-1ty2C01	C:102-209
1b	Stap_Strp_tox_C-1ty2C02	C:102-209
1c	Stap_Strp_tox_C-1ty2C03	C:102-209

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

Family: Stap_Strp_toxin (39)

Streptococcus pyogenes (4)

2a	Stap_Strp_toxin-1ty2C04	C:15-94
2b	Stap_Strp_toxin-1ty2C05	C:15-94
2c	Stap_Strp_toxin-1ty2C06	C:15-94

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (Q7BAE3_STRPY | Q7BAE3)

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.

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(no "Related Entries Specified in the PDB File" available for 1TY2)

Description

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Ligands, Modified Residues, Ions (1, 3)

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