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(-) Description

Title :  VCA0105 PAAR-REPEAT PROTEIN FROM VIBRIO CHOLERAE IN COMPLEX WITH A VGRG-LIKE BETA-HELIX THAT IS BASED ON A FRAGMENT OF T4 GP5
 
Authors :  S. A. Buth, P. G. Leiman, M. M. Shneider
Date :  07 Mar 13  (Deposition) - 14 Aug 13  (Release) - 11 Jun 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Paar-Repeat Motif, Membrane Piercing, Type Vi Secretion System, Vibrio Cholerae Vgrg2, Cell Puncturing Device, Beta-Helix, T4 Gp5, Vgrg Tip, T6Ss Spike, Hydrolase-Protein Binding Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. M. Shneider, S. A. Buth, B. T. Ho, M. Basler, J. J. Mekalanos, P. G. Leiman
Paar-Repeat Proteins Sharpen And Diversify The Type Vi Secretion System Spike.
Nature V. 500 350 2013
PubMed-ID: 23925114  |  Reference-DOI: 10.1038/NATURE12453

(-) Compounds

Molecule 1 - TAIL-ASSOCIATED LYSOZYME
    Chains: A, B, C
    EC Number: 3.2.1.17
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PEEVA2, A PET-23A DERIVATIVE
    Expression System Strain: B834
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: GP5G484, UNP RESIDUES 484-575
    Gene: 5
    Mutation: YES
    Organism Scientific: ENTEROBACTERIA PHAGE T4
    Organism Taxid: 10665
    Synonym: PROTEIN GP5, GP5*, GP5C
 
Molecule 2 - PUTATIVE UNCHARACTERIZED PROTEIN
    Chains: D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PATE, A PACYCDUET-1 DERIVATIVE
    Expression System Strain: B834
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: VC_A0105
    Organism Scientific: VIBRIO CHOLERAE O1 BIOVAR ELTOR
    Organism Taxid: 243277
    Strain: N16961
    Synonym: VCA0105

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 5)

Asymmetric/Biological Unit (5, 5)
No.NameCountTypeFull Name
1ELA1Ligand/Ion9-OCTADECENOIC ACID
2MG1Ligand/IonMAGNESIUM ION
3PLM1Ligand/IonPALMITIC ACID
4STE1Ligand/IonSTEARIC ACID
5ZN1Ligand/IonZINC ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:701 , HOH A:702 , HOH B:722 , HOH B:751 , HOH C:702 , HOH C:794BINDING SITE FOR RESIDUE MG A 601
2AC2SOFTWAREILE A:496 , ILE A:504 , ILE C:496BINDING SITE FOR RESIDUE PLM A 602
3AC3SOFTWAREILE A:512 , HOH A:813 , ILE B:496 , ILE B:512 , ILE C:496 , VAL C:502 , GLN C:526BINDING SITE FOR RESIDUE STE B 601
4AC4SOFTWARETHR A:495 , HOH A:815 , ILE B:504 , LYS C:488 , ILE C:512BINDING SITE FOR RESIDUE ELA C 601
5AC5SOFTWAREHIS D:14 , HIS D:46 , HIS D:54 , CYS D:81BINDING SITE FOR RESIDUE ZN D 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4JIV)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4JIV)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4JIV)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4JIV)

(-) Exons   (0, 0)

(no "Exon" information available for 4JIV)

(-) Sequences/Alignments

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:93
                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee...eeeee...eeeee...eeeee...eeeee...eeeee...eeeee...eeeee..eeeeee.eeeeee..eeeee...eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                 4jiv A 483 SGDETKTVEGNGTILVKGNVTIIVEGNADITVKGDATTLVEGNQTNTVNGNLSWKVAGTVDWDVGGDWTEKMASMSSISSGQYHIVGSAINLN 575
                                   492       502       512       522       532       542       552       562       572   


Chain B from PDB  Type:PROTEIN  Length:93
                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee...eeeee...eeeee...eeeee...eeeee...eeeee...eeeee...eeeee..eeeeee.eeeeee..eeeee..eeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                 4jiv B 483 SGDETKTVEGNGTILVKGNVTIIVEGNADITVKGDATTLVEGNQTNTVNGNLSWKVAGTVDWDVGGDWTEKMASMSSISSGQYHIVGSAINLN 575
                                   492       502       512       522       532       542       552       562       572   


Chain C from PDB  Type:PROTEIN  Length:93
                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee...eeeee...eeeee...eeeee...eeeee...eeeee...eeeee...eeeee..eeeeee.eeeeee...eeee..eeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                 4jiv C 483 SGDETKTVEGNGTILVKGNVTIIVEGNADITVKGDATTLVEGNQTNTVNGNLSWKVAGTVDWDVGGDWTEKMASMSSISSGQYHIVGSAINLN 575
                                   492       502       512       522       532       542       552       562       572   


Chain D from PDB  Type:PROTEIN  Length:93
                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........ee........ee.......eee..ee......eeeeeee..eeeeeee.......eee..ee.............ee....eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                 4jiv D   2 GNGIVVGHLGTDHDGFPPTPVTAGSATVRYDGIPAARLGDPLAPHDKPKHPSHGRAIAAGSGTVMIDGKPAARVGDAVDCGGVLQGASSVNIG  94
                                    11        21        31        41        51        61        71        81        91
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4JIV)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4JIV)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4JIV)

(-) Gene Ontology  (20, 20)

Asymmetric/Biological Unit(hide GO term definitions)

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  Q9KN60_VIBCH | Q9KN60
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        BP5_BPT4 | P16009: 1k28 1pdl 1wth 2z6b 3a1m 4jiw 4jj2 4ku0 4osd 5iv5

(-) Related Entries Specified in the PDB File

1k28 THE STRUCTURE OF THE FULL LENGTH GP5 PROTEIN FROM PHAGE T4
4jiw