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Title :   STRUCTURE AND FUNCTIONAL CHARACTERIZATION OF A VIBRIO CHOLERAE TOXIN FROM THE MARTX/VGRG FAMILY.

Authors :   E. Durand, G. Audoly, E. Derrez, S. Spinelli, M. Ortiz-Lombardia, E. Ca D. Raoult, C. Cambillau

Date :   21 Feb 12 (Deposition) - 29 Aug 12 (Release) - 29 Aug 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

Keywords :   Alpha-Beta Protein, Actin Crosslinking Domain (Acd), G-Actin, Toxin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. Durand, G. Audoly, E. Derrez, S. Spinelli, M. Ortiz-Lombardia, E. Cascales, D. Raoult, C. Cambillau
Structure And Functional Characterization Of A Vibrio Cholerae Toxin From The Martx/Vgrg Family.
J. Biol. Chem. 2012
PubMed: search

Compounds

Molecule 1 - VGRG PROTEIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PETG-20A
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 716-1111
	Gene	:	VC_1416, VGRG1
	Organism Scientific	:	VIBRIO CHOLERAE
	Organism Taxid	:	666
	Strain	:	O395

Structural Features

Chains, Units

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

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (2, 9)

Asymmetric Unit (2, 9)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL
2	MSE	8	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (2, 9)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL
2	MSE	8	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (2, 18)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	MSE	16	Mod. Amino Acid	SELENOMETHIONINE

Sites (1, 1)

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:50 , GLY A:55 , SER A:56 , HIS A:75 , HOH A:535 , HOH A:641	BINDING SITE FOR RESIDUE GOL A 401

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ACD	PS51772	Actin cross-linking (ACD) domain profile.	VGRG1_VIBC3	712-1095	1	A:1-354
1	ACD	PS51772	Actin cross-linking (ACD) domain profile.	VGRG1_VIBCH	728-1163	1	A:1-354

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ACD	PS51772	Actin cross-linking (ACD) domain profile.	VGRG1_VIBC3	712-1095	1	A:1-354
1	ACD	PS51772	Actin cross-linking (ACD) domain profile.	VGRG1_VIBCH	728-1163	1	A:1-354

Biological Unit 2 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ACD	PS51772	Actin cross-linking (ACD) domain profile.	VGRG1_VIBC3	712-1095	2	A:1-354
1	ACD	PS51772	Actin cross-linking (ACD) domain profile.	VGRG1_VIBCH	728-1163	2	A:1-354

Exons (0, 0)

Sequences/Alignments

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:357
 aligned with VGRG1_VIBC3 | A0A0H3AIG7 from UniProtKB/Swiss-Prot  Length:1095

    Alignment length:357
                                   718       728       738       748       758       768       778       788       798       808       818       828       838       848       858       868       878       888       898       908       918       928       938       948       958       968       978       988       998      1008      1018      1028      1038      1048      1058       
         VGRG1_VIBC3    709 TKATPDFPTHFPKSSIGIENELAGLVVAMPANSAQKFGYVKSAQGDALFMLTKDMNQGSYQRPPSLQDGKNYQNWQTHTVELVSYPCEMDDKAAVETRKQAMLWLATHFTTHIDQSNHQPLAPIQSEDGRFVIEITNAKHVIAAGNGISAESQGQTITMTPSGQQATVGVAAKGFGTSATPELRLLESAPWYQKSLKSQFASLTSAENLDDKELAANVFAYLTSIYLKTAELAKKFGIYINEWDPMSEQITPNANGLTDPKVKNAWEILPRTKPSKIVEILSKSDAKAVMKHIKPQLQSRYSESLSKNVFQYFQDGGEVAGHGINNATVGDKHSPELAILFEFRTVPNELQSYLPKT 1065
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........ee..eeeeeeee...eeeeee.....eeeeeee....eeeeeeeeeeeee...hhhhh.......eeeeeeeeee..ee..hhhhhhhhhhhhhhhhhhhhhhhhhh..............eeeee.....eeee...................eeeeeeee.hhh....hhhhhhhhh......hhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhh.........hhhhhhhhheee..hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh............eee....eeeeeeeee......hhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---ACD  PDB: A:1-354 UniProt: 712-1095                                                                                                                                                                                                                                                                                                                                PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4dtd A   -2 TKATPDFPTHFPKSSIGIENELAGLVVAmPANSAQKFGYVKSAQGDALFmLTKDmNQGSYQRPPSLQDGKNYQNWQTHTVELVSYPCEmDDKAAVETRKQAmLWLATHFTTHIDQSNHQPLAPIQSEDGRFVIEITNAKHVIAAGNGISAESQGQTITmTPSGQQATVGVAAKGFGTSATPELRLLESAPWYQKSLKSQFASLTSAENLDDKELAANVFAYLTSIYLKTAELAKKFGIYINEWDPmSEQITPNANGLTDPKVKNAWEILPRTKPSKIVEILSKSDAKAVmKHIKPQLQSRYSESLSKNVFQYFQDGGEVAGHGINNATVGDKHSPELAILFEFRTVPNELQSYLPKT  354
                                     7        17        27        37        47    |   57        67        77        87        97 |     107       117       127       137       147       157       167       177       187       197       207       217       227       237     | 247       257       267       277       287       297       307       317       327       337       347       
                                                       26-MSE               47-MSE|                                86-MSE       99-MSE                                                  156-MSE                                                                                243-MSE                                     287-MSE                                                               
                                                                                 52-MSE

Chain A from PDB  Type:PROTEIN  Length:357
 aligned with VGRG1_VIBCH | Q9KS45 from UniProtKB/Swiss-Prot  Length:1163

    Alignment length:357
                                   734       744       754       764       774       784       794       804       814       824       834       844       854       864       874       884       894       904       914       924       934       944       954       964       974       984       994      1004      1014      1024      1034      1044      1054      1064      1074       
         VGRG1_VIBCH    725 TKATPDFPTHFPKSSIGIENELAGLVVAMPANSAQKFGYVKSAQGDALFMLTKDMNQGSYQRPPSLQDGKNYQNWQTHTVELVSYPCEMDDKAAVETRKQAMLWLATHFTTHIDQSNHQPLAPIQSEDGRFVIEITNAKHVIAAGNGISAESQGQTITMTPSGQQATVGVAAKGFGTSATPELRLLESAPWYQKSLKSQFASLTSAENLDDKELAANVFAYLTSIYLKTAELAKKFGIYINEWDPMSEQITPNANGLTDPKVKNAWEILPRTKPSKIVEILSKSDAKAVMKHIKPQLQSRYSESLSKNVFQYFQDGGEVAGHGINNATVGDKHSPELAILFEFRTVPNELQSYLPKT 1081
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........ee..eeeeeeee...eeeeee.....eeeeeee....eeeeeeeeeeeee...hhhhh.......eeeeeeeeee..ee..hhhhhhhhhhhhhhhhhhhhhhhhhh..............eeeee.....eeee...................eeeeeeee.hhh....hhhhhhhhh......hhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhh.........hhhhhhhhheee..hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh............eee....eeeeeeeee......hhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ---ACD  PDB: A:1-354 UniProt: 728-1163                                                                                                                                                                                                                                                                                                                                PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4dtd A   -2 TKATPDFPTHFPKSSIGIENELAGLVVAmPANSAQKFGYVKSAQGDALFmLTKDmNQGSYQRPPSLQDGKNYQNWQTHTVELVSYPCEmDDKAAVETRKQAmLWLATHFTTHIDQSNHQPLAPIQSEDGRFVIEITNAKHVIAAGNGISAESQGQTITmTPSGQQATVGVAAKGFGTSATPELRLLESAPWYQKSLKSQFASLTSAENLDDKELAANVFAYLTSIYLKTAELAKKFGIYINEWDPmSEQITPNANGLTDPKVKNAWEILPRTKPSKIVEILSKSDAKAVmKHIKPQLQSRYSESLSKNVFQYFQDGGEVAGHGINNATVGDKHSPELAILFEFRTVPNELQSYLPKT  354
                                     7        17        27        37        47    |   57        67        77        87        97 |     107       117       127       137       147       157       167       177       187       197       207       217       227       237     | 247       257       267       277       287       297       307       317       327       337       347       
                                                       26-MSE               47-MSE|                                86-MSE       99-MSE                                                  156-MSE                                                                                243-MSE                                     287-MSE                                                               
                                                                                 52-MSE

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	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 '\|'

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (15, 15)

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Description