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Asym./Biol. Unit (Jmol Viewer)

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

Title :   STRUCTURAL ANALYSIS OF HOMODIMERIC STAPHYLOCOCCAL AUREUS VIRULENCE FACTOR ESXA

Authors :   R. Sundaramoorthy, P. K. Fyfe, W. N. Hunter

Date :   17 Apr 08 (Deposition) - 26 Aug 08 (Release) - 25 Aug 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.40

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

Keywords :   Secreted, Virulence, Four Helical Bundle, Cell Invasion (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Sundaramoorthy, P. K. Fyfe, W. N. Hunter
Structure Of Staphylococcus Aureus Esxa Suggests A Contribution To Virulence By Action As A Transport Chaperone And/Or Adaptor Protein.
J. Mol. Biol. V. 383 603 2008
PubMed-ID: 18773907 | Reference-DOI: 10.1016/J.JMB.2008.08.047

Molecule 1 - VIRULENCE FACTOR ESXA
	Atcc	:	700699
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Organism Scientific	:	STAPHYLOCOCCUS AUREUS
	Organism Taxid	:	1280
	Other Details	:	GENOMIC DNA
	Strain	:	MU50

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 9)

No.	Name	Count	Type	Full Name
1	CAC	1	Ligand/Ion	CACODYLATE ION
2	MSE	3	Mod. Amino Acid	SELENOMETHIONINE
3	ZN	5	Ligand/Ion	ZINC ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:85 , GLY B:19 , GLN B:20 , ASP B:23 , GLU B:70 , LYS B:73 , ZN B:1089 , HOH B:2078 , HOH B:2079	BINDING SITE FOR RESIDUE CAC B1088
2	AC2	SOFTWARE	GLU A:38 , GLU A:53 , GLU B:10	BINDING SITE FOR RESIDUE ZN A1086
3	AC3	SOFTWARE	GLU A:10 , SER A:49 , GLU A:52 , HOH A:2091 , GLU B:38	BINDING SITE FOR RESIDUE ZN A1087
4	AC4	SOFTWARE	ASP A:23 , HOH A:2092 , HOH A:2093 , GLU B:53 , GLU B:85	BINDING SITE FOR RESIDUE ZN A1088
5	AC5	SOFTWARE	GLU A:85 , GLY B:19 , ASP B:23 , GLU B:70 , CAC B:1088 , HOH B:2079	BINDING SITE FOR RESIDUE ZN B1089
6	AC6	SOFTWARE	GLU A:44 , HOH A:2094 , HOH A:2095 , ASP B:31	BINDING SITE FOR RESIDUE ZN A1089

(no "SS Bond" information available for 2VS0)

(no "Cis Peptide Bond" information available for 2VS0)

(no "SAP(SNP)/Variant" information available for 2VS0)

(no "PROSITE Motif" information available for 2VS0)

(no "Exon" information available for 2VS0)

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:83
 aligned with ESXA_STAA8 | Q2G189 from UniProtKB/Swiss-Prot  Length:97

    Alignment length:83
                                    12        22        32        42        52        62        72        82   
            ESXA_STAA8    3 MIKMSPEEIRAKSQSYGQGSDQIRQILSDLTRAQGEIAANWEGQAFSRFEEQFQQLSPKVEKFAQLLEEIKQQLNSTADAVQE 85
               SCOP domains d2vs0a_ A: automated matches                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------- Transcript
                  2vs0 A  3 mIKmSPEEIRAKSQSYGQGSDQIRQILSDLTRAQGEIAANWEGQAFSRFEEQFQQLSPKVEKFAQLLEEIKQQLNSTADAVQE 85
                            |  |    12        22        32        42        52        62        72        82   
                            |  |                                                                               
                            3-MSE                                                                              
                               6-MSE

Chain A from PDB  Type:PROTEIN  Length:83
 aligned with ESXA_STAAM | Q99WU4 from UniProtKB/Swiss-Prot  Length:97

    Alignment length:83
                                    12        22        32        42        52        62        72        82   
            ESXA_STAAM    3 MIKMSPEEIRAKSQSYGQGSDQIRQILSDLTRAQGEIAANWEGQAFSRFEEQFQQLSPKVEKFAQLLEEIKQQLNSTADAVQE 85
               SCOP domains d2vs0a_ A: automated matches                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------- Transcript
                  2vs0 A  3 mIKmSPEEIRAKSQSYGQGSDQIRQILSDLTRAQGEIAANWEGQAFSRFEEQFQQLSPKVEKFAQLLEEIKQQLNSTADAVQE 85
                            |  |    12        22        32        42        52        62        72        82   
                            3-MSE                                                                              
                               6-MSE

Chain B from PDB  Type:PROTEIN  Length:84
 aligned with ESXA_STAA8 | Q2G189 from UniProtKB/Swiss-Prot  Length:97

    Alignment length:84
                                    13        23        33        43        53        63        73        83    
            ESXA_STAA8    4 IKMSPEEIRAKSQSYGQGSDQIRQILSDLTRAQGEIAANWEGQAFSRFEEQFQQLSPKVEKFAQLLEEIKQQLNSTADAVQEQD 87
               SCOP domains d2vs0b_ B: automated matches                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) WXG100-2vs0B01 B:4-87                                                                Pfam domains (1)
           Pfam domains (2) WXG100-2vs0B02 B:4-87                                                                Pfam domains (2)
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------ Transcript
                  2vs0 B  4 IKmSPEEIRAKSQSYGQGSDQIRQILSDLTRAQGEIAANWEGQAFSRFEEQFQQLSPKVEKFAQLLEEIKQQLNSTADAVQEQD 87
                              |     13        23        33        43        53        63        73        83    
                              6-MSE

Chain B from PDB  Type:PROTEIN  Length:84
 aligned with ESXA_STAAM | Q99WU4 from UniProtKB/Swiss-Prot  Length:97

    Alignment length:84
                                    13        23        33        43        53        63        73        83    
            ESXA_STAAM    4 IKMSPEEIRAKSQSYGQGSDQIRQILSDLTRAQGEIAANWEGQAFSRFEEQFQQLSPKVEKFAQLLEEIKQQLNSTADAVQEQD 87
               SCOP domains d2vs0b_ B: automated matches                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) WXG100-2vs0B01 B:4-87                                                                Pfam domains (1)
           Pfam domains (2) WXG100-2vs0B02 B:4-87                                                                Pfam domains (2)
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------ Transcript
                  2vs0 B  4 IKmSPEEIRAKSQSYGQGSDQIRQILSDLTRAQGEIAANWEGQAFSRFEEQFQQLSPKVEKFAQLLEEIKQQLNSTADAVQEQD 87
                              |     13        23        33        43        53        63        73        83    
                              6-MSE

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: Ferritin-like (533)

Superfamily: EsxAB dimer-like (17)

Family: automated matches (13)

Protein domain: automated matches (13)

Staphylococcus aureus [TaxId: 1280] (2)

1a	d2vs0a_	A:
1b	d2vs0b_	B:

(no "CATH Domain" information available for 2VS0)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: EsxAB (5)

Family: WXG100 (5)

Staphylococcus aureus (strain Mu50 / ATCC 700699) (2)

1a	WXG100-2vs0B01	B:4-87
1b	WXG100-2vs0B02	B:4-87

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (ESXA_STAAM | Q99WU4)

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.

Chain A,B (ESXA_STAA8 | Q2G189)

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
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		MSE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
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		AC6	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2vs0)

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		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
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	ESXA_STAA8 \| Q2G189
		Comparative Protein Structure Models	:	ModBase
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		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	ESXA_STAAM \| Q99WU4
		Comparative Protein Structure Models	:	ModBase
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		Protein-protein Interaction	:	DIP
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	ESXA_STAA8 \| Q2G189
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	ESXA_STAAM \| Q99WU4
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	ESXA_STAA8 \| Q2G189	:	2vrz
	ESXA_STAAM \| Q99WU4	:	2vrz

2vrz	STRUCTURAL ANALYSIS OF HOMODIMERIC STAPHYLOCOCCAL AUREUS ESXA

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 9)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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SCOP Domains (1, 2)

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