2AQ2 - JenaLib

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Title :   CRYSTAL STRUCTURE OF T-CELL RECEPTOR V BETA DOMAIN VARIANT COMPLEXED WITH SUPERANTIGEN SEC3 MUTANT

Authors :   S. Cho, C. P. Swaminathan, J. Yang, M. C. Kerzic, R. Guan, M. C. Kieke, D. M. Kranz, R. A. Mariuzza, E. J. Sundberg

Date :   17 Aug 05 (Deposition) - 21 Mar 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   T-Cell Receptor V Beta Domain, Staphlococcal Enterotoxin C3, Complex Structure, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Cho, C. P. Swaminathan, J. Yang, M. C. Kerzic, R. Guan, M. C. Kieke, D. M. Kranz, R. A. Mariuzza, E. J. Sundberg
Structural Basis Of Affinity Maturation And Intramolecular Cooperativity In A Protein-Protein Interaction.
Structure V. 13 1775 2005
PubMed-ID: 16338399 | Reference-DOI: 10.1016/J.STR.2005.08.015
(for further references see the PDB file header)

Molecule 1 - T-CELL RECEPTOR BETA CHAIN V
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PT7-7
	Expression System Strain	:	BL21(DE3)PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

Molecule 2 - ENTEROTOXIN TYPE C-3
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	ENTC3
	Organism Scientific	:	STAPHYLOCOCCUS AUREUS
	Organism Taxid	:	1280
	Synonym	:	SEC3

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 9)

No.	Name	Count	Type	Full Name
1	NA	3	Ligand/Ion	SODIUM ION
2	SO4	5	Ligand/Ion	SULFATE ION
3	ZN	1	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 5)

No.	Name	Count	Type	Full Name
1	NA	-1	Ligand/Ion	SODIUM ION
2	SO4	5	Ligand/Ion	SULFATE ION
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (1, 5)

No.	Name	Count	Type	Full Name
1	NA	-1	Ligand/Ion	SODIUM ION
2	SO4	5	Ligand/Ion	SULFATE ION
3	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP B:83 , HIS B:116 , HIS B:120	BINDING SITE FOR RESIDUE ZN B 1001
2	AC2	SOFTWARE	GLU A:1 , PHE B:174 , ASN B:175	BINDING SITE FOR RESIDUE NA B 1002
3	AC3	SOFTWARE	LYS B:25 , PHE B:174	BINDING SITE FOR RESIDUE NA B 1003
4	AC4	SOFTWARE	TYR B:77 , THR B:114 , LYS B:115 , HOH B:1150	BINDING SITE FOR RESIDUE NA B 1004
5	AC5	SOFTWARE	TYR A:33 , HOH A:174 , HIS B:47 , ASN B:70 , GLU B:71	BINDING SITE FOR RESIDUE SO4 B 500
6	AC6	SOFTWARE	HOH A:131 , TYR B:26 , HIS B:31 , ASP B:55 , ASN B:60 , ASN B:88 , TYR B:90 , HOH B:1050 , HOH B:1086 , HOH B:1088	BINDING SITE FOR RESIDUE SO4 B 501
7	AC7	SOFTWARE	LYS B:75 , ARG B:138 , HOH B:1038 , HOH B:1142	BINDING SITE FOR RESIDUE SO4 B 502
8	AC8	SOFTWARE	LYS B:75 , LYS B:78 , ARG B:138 , HOH B:1059	BINDING SITE FOR RESIDUE SO4 B 503
9	AC9	SOFTWARE	GLY B:203 , ASP B:204 , LYS B:205 , HOH B:1151	BINDING SITE FOR RESIDUE SO4 B 504

Asymmetric Unit

No.	Residues
1	A:23	-	A:92
2	B:93	-	B:108

Asymmetric Unit

No.	Residues
1	Ser A:7	-	Pro A:8

(no "SAP(SNP)/Variant" information available for 2AQ2)

Asymmetric Unit (2, 2)

	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	1	B:110-119
2	STAPH_STREP_TOXIN_2	PS00278	Staphyloccocal enterotoxin/Streptococcal pyrogenic exotoxin signature 2.	ENTC3_STAAU	178-201	1	B:149-172

Biological Unit 1 (2, 2)

	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	1	B:110-119
2	STAPH_STREP_TOXIN_2	PS00278	Staphyloccocal enterotoxin/Streptococcal pyrogenic exotoxin signature 2.	ENTC3_STAAU	178-201	1	B:149-172

Biological Unit 2 (2, 2)

	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	1	B:110-119
2	STAPH_STREP_TOXIN_2	PS00278	Staphyloccocal enterotoxin/Streptococcal pyrogenic exotoxin signature 2.	ENTC3_STAAU	178-201	1	B:149-172

(no "Exon" information available for 2AQ2)

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:110
 aligned with TVB5_MOUSE | P04213 from UniProtKB/Swiss-Prot  Length:122

    Alignment length:114
                                    18        28        38        48        58        68        78        88        98       108       118    
           TVB5_MOUSE     9 EAAVTQSPRSKVAVTGGKVTLSCHQTNNHDYMYWYRQDTGHGLRLIHYSYVADSTEKGDIPDGYKASRPSQENFSLILELASLSQTAVYFCASSGTGGALDTQYFGPGTRLLVL 122
               SCOP domains d2aq2a1 A:1-117 T-cell antigen receptor                                                                            SCOP domains
               CATH domains 2aq2A00 A:1-117 Immunoglobulins                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.....eeeeeee.....eeeeeee......ee.......eeeeee..eeeeee...hhhhheeeeeeeee..----eeee...eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 2aq2 A   1 EAAVTQSPRNKVAVTGEKVTLSCQQTNNHNNMYWYRQDTGHGLRLIHYSYGVGNTEKGDIPDGYEASRPSQEQFSLILESATPSQTSVYFCASGGGG----TLYFGAGTRLSVL 117
                                    10        20        30        40        50        60  ||    71        81        91      |  - | ||  113    
                                                                                         63|                               98   99 ||         
                                                                                          65                                     101|         
                                                                                                                                  108

Chain B from PDB  Type:PROTEIN  Length:234
 aligned with ENTC3_STAAU | P0A0L5 from UniProtKB/Swiss-Prot  Length:266

    Alignment length:236
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258      
          ENTC3_STAAU    29 SQPDPMPDDLHKSSEFTGTMGNMKYLYDDHYVSATKVKSVDKFLAHDLIYNISDKKLKNYDKVKTELLNEDLAKKYKDEVVDVYGSNYYVNCYFSSKDNVGKVTGGKTCMYGGITKHEGNHFDNGNLQNVLVRVYENKRNTISFEVQTDKKSVTAQELDIKARNFLINKKNLYEFNSSPYETGYIKFIENNGNTFWYDMMPAPGDKFDQSKYLMMYNDNKTVDSKSVKIEVHLTTK 264
               SCOP domains d2aq2b1 B:2-116 Staphylococcal enterotoxin C3, SEC3                                                                  d2aq2b2 B:117-235 Staphylococcal enterotoxin C3, SEC3                                                                   SCOP domains
               CATH domains 2aq2B01 B:2-31,B:118-235      2aq2B02 B:32-117  [code=2.40.50.110, no name defined]                                   2aq2B01 B:2-31,B:118-235  [code=3.10.20.120, no name defined]                                                          CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhh.hhhhh...hhhhhh......eeeeee.........eeee.........eeeeeee..hhhhhhhhh...eeeee..................--eeeeee..eee...........eeeeeeeee..eeeeeeeeee...eeehhhhhhhhhhhhhhhhh........eeeeeeeee.....eeeee.........hhhhhhhhhhhh.eee....eeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------STAPH_STRE-----------------------------STAPH_STREP_TOXIN_2     --------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2aq2 B   2 SQPDPMPDDLHKSSEFTGTMGNMKYLYDDHYVSATKVKSVDKFLAHDLIYNISDKKLKNYDKVKTELLNEDLAKKYKDEVVDVYGSNYYVNCYFSSKDNVWWP--GKTCMYGGITKHEGNHFDNGNLQNVLVRVYENKRNTISFEVQTDKKSVTAQELDIKARNFLINKKNLYEFNSSPYETGYIKFIENNGNTFWYDMMPAPGDKFDQSKYLMMYNDNKTVDSKSVKIEVHLTTK 235
                                    11        21        31        41        51        61        71        81        91       101  |  | 109       119       129       139       149       159       169       179       189       199       209       219       229      
                                                                                                                                104  |                                                                                                                                  
                                                                                                                                   105

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 "Pfam Domain" information available for 2AQ2)

Asymmetric Unit(hide GO term definitions)

Chain A (TVB5_MOUSE | P04213)

Chain B (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.

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	Cis Peptide Bonds
		Ser A:7 - Pro A:8	[ RasMol ]

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2apb	THE G17E/S54N/L81S VARIANT OF THE MURINE T CELL RECEPTOR V BETA 8.2 DOMAIN
2apf	THE G17E/A52V/S54N/K66E/L81S VARIANT OF THE MURINE T CELL RECEPTOR V BETA 8.2 DOMAIN
2apt	THE G17E/S54N/K66E/Q72H/E80V/L81S/T87S/G96V VARIANT OF THE MURINE T CELL RECEPTOR V BETA 8.2 DOMAIN
2apv	THE G17E/A52V/S54N/Q72H/E80V/L81S/T87S/G96V VARIANT OF THE MURINE T CELL RECEPTOR V BETA 8.2 DOMAIN
2apw	THE G17E/A52V/S54N/K66E/E80V/L81S/T87S/G96V VARIANT OF THE MURINE T CELL RECEPTOR V BETA 8.2 DOMAIN
2apx	THE G17E/A52V/S54N/K66E/Q72H/E80V/L81S/T87S/G96V VARIANT OF THE MURINE T CELL RECEPTOR V BETA 8.2 DOMAIN
2aq1	T-CELL RECEPTOR V BETA DOMAIN VARIANT (G17E/A52V/S54N/K66E/ E80V/L81S/T87S/G96V) COMPLEXED WITH SUPERANTIGEN SEC3 MUTANT
2aq3	T-CELL RECEPTOR V BETA DOMAIN VARIANT (G17E/L81S) COMPLEXED WITH SUPERANTIGEN SEC3 MUTANT

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 9)

Sites (9, 9)

SS Bonds (2, 2)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 2)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (3, 3)

CATH Domains (3, 3)

Pfam Domains (0, 0)

Gene Ontology (2, 2)

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