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(-) Description

Title :  CRYSTAL STRUCTURE OF VIRB8 FROM BRUCELLA SUIS
 
Authors :  M. Coincon, M. A. Smith, J. Sygusch, C. Baron
Date :  29 Feb 12  (Deposition) - 05 Sep 12  (Release) - 05 Sep 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym. Unit :  A,B,C,D,E
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  E  (1x)
Keywords :  Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. A. Smith, M. Coincon, A. Paschos, B. Jolicoeur, P. Lavallee, J. Sygusch, C. Baron
Identification Of The Binding Site Of Brucella Virb8 Interaction Inhibitors.
Chem. Biol. V. 19 1041 2012
PubMed-ID: 22921071  |  Reference-DOI: 10.1016/J.CHEMBIOL.2012.07.007

(-) Compounds

Molecule 1 - TYPE IV SECRETION SYSTEM PROTEIN VIRB8
    Chains: A, B, C, D, E
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: STAR
    Expression System Vector: PET24D
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 97-234
    Organism Scientific: BRUCELLA SUIS
    Organism Taxid: 29461

 Structural Features

(-) Chains, Units

  12345
Asymmetric Unit : ABCDE
Biological Unit 1 (1x): A    
Biological Unit 2 (1x):  B   
Biological Unit 3 (1x):   C  
Biological Unit 4 (1x):    D 
Biological Unit 5 (1x):     E

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 4AKZ)

(-) Sites  (0, 0)

(no "Site" information available for 4AKZ)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4AKZ)

(-) 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:138
 aligned with VIRB8_BRUSU | Q7CEG3 from UniProtKB/Swiss-Prot  Length:239

    Alignment length:138
                                   106       116       126       136       146       156       166       176       186       196       206       216       226        
          VIRB8_BRUSU    97 SYDTVMDKYWLSQYVIARETYDWYTLQKDYETVGMLSSPSEGQSYASQFQGDKALDKQYGSNVRTSVTIVSIVPNGKGIGTVRFAKTTKRTNETGDGETTHWIATIGYQYVNPSLMSESARLTNPLGFNVTSYRVDPE 234
               SCOP domains d4akza_ A: Type IV secretion system protein VirB8                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhh..eeeeeeeeeeee....eeeeeeeeeeee.......eeeeeeeeeeeee.hhhhhhhhhhh.....eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4akz A  97 SYDTVMDKYWLSQYVIARETYDWYTLQKDYETVGMLSSPSEGQSYASQFQGDKALDKQYGSNVRTSVTIVSIVPNGKGIGTVRFAKTTKRTNETGDGETTHWIATIGYQYVNPSLMSESARLTNPLGFNVTSYRVDPE 234
                                   106       116       126       136       146       156       166       176       186       196       206       216       226        


Chain B from PDB  Type:PROTEIN  Length:134
 aligned with VIRB8_BRUSU | Q7CEG3 from UniProtKB/Swiss-Prot  Length:239

    Alignment length:138
                                   106       116       126       136       146       156       166       176       186       196       206       216       226        
          VIRB8_BRUSU    97 SYDTVMDKYWLSQYVIARETYDWYTLQKDYETVGMLSSPSEGQSYASQFQGDKALDKQYGSNVRTSVTIVSIVPNGKGIGTVRFAKTTKRTNETGDGETTHWIATIGYQYVNPSLMSESARLTNPLGFNVTSYRVDPE 234
               SCOP domains d4akzb_ B: Type IV secretion system protein VirB8                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhh..eeeeeeeeeeee....eeeeeeeeeeee.----..eeeeeeeeeeeee.hhhhh..hhhhh....eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4akz B  97 SYDTVMDKYWLSQYVIARETYDWYTLQKDYETVGMLSSPSEGQSYASQFQGDKALDKQYGSNVRTSVTIVSIVPNGKGIGTVRFAKTTKRT----DGETTHWIATIGYQYVNPSLMSESARLTNPLGFNVTSYRVDPE 234
                                   106       116       126       136       146       156       166       176       186|    | 196       206       216       226        
                                                                                                                    187  192                                          


Chain C from PDB  Type:PROTEIN  Length:134
 aligned with VIRB8_BRUSU | Q7CEG3 from UniProtKB/Swiss-Prot  Length:239

    Alignment length:138
                                   106       116       126       136       146       156       166       176       186       196       206       216       226        
          VIRB8_BRUSU    97 SYDTVMDKYWLSQYVIARETYDWYTLQKDYETVGMLSSPSEGQSYASQFQGDKALDKQYGSNVRTSVTIVSIVPNGKGIGTVRFAKTTKRTNETGDGETTHWIATIGYQYVNPSLMSESARLTNPLGFNVTSYRVDPE 234
               SCOP domains d4akzc_ C: Type IV secretion system protein VirB8                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh.hhhhhhhhhhhhh...hhhhhh...eeeeeeeeeeee....eeeeeeeeeeee.----..eeeeeeeeeeeee.hhhhh..hhhhh....eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4akz C  97 SYDTVMDKYWLSQYVIARETYDWYTLQKDYETVGMLSSPSEGQSYASQFQGDKALDKQYGSNVRTSVTIVSIVPNGKGIGTVRFAKTTKRT----DGETTHWIATIGYQYVNPSLMSESARLTNPLGFNVTSYRVDPE 234
                                   106       116       126       136       146       156       166       176       186|    | 196       206       216       226        
                                                                                                                    187  192                                          


Chain D from PDB  Type:PROTEIN  Length:133
 aligned with VIRB8_BRUSU | Q7CEG3 from UniProtKB/Swiss-Prot  Length:239

    Alignment length:138
                                   106       116       126       136       146       156       166       176       186       196       206       216       226        
          VIRB8_BRUSU    97 SYDTVMDKYWLSQYVIARETYDWYTLQKDYETVGMLSSPSEGQSYASQFQGDKALDKQYGSNVRTSVTIVSIVPNGKGIGTVRFAKTTKRTNETGDGETTHWIATIGYQYVNPSLMSESARLTNPLGFNVTSYRVDPE 234
               SCOP domains d4akzd_ D: Type IV secretion system protein VirB8                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhee..hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhh..eeeeeeeeeeee....eeeeeeeeeeee.-----.eeeeeeeeeeeee.hhhhhhhhhhhhh...eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4akz D  97 SYDTVMDKYWLSQYVIARETYDWYTLQKDYETVGMLSSPSEGQSYASQFQGDKALDKQYGSNVRTSVTIVSIVPNGKGIGTVRFAKTTKRT-----GETTHWIATIGYQYVNPSLMSESARLTNPLGFNVTSYRVDPE 234
                                   106       116       126       136       146       156       166       176       186|     |196       206       216       226        
                                                                                                                    187   193                                         


Chain E from PDB  Type:PROTEIN  Length:134
 aligned with VIRB8_BRUSU | Q7CEG3 from UniProtKB/Swiss-Prot  Length:239

    Alignment length:138
                                   106       116       126       136       146       156       166       176       186       196       206       216       226        
          VIRB8_BRUSU    97 SYDTVMDKYWLSQYVIARETYDWYTLQKDYETVGMLSSPSEGQSYASQFQGDKALDKQYGSNVRTSVTIVSIVPNGKGIGTVRFAKTTKRTNETGDGETTHWIATIGYQYVNPSLMSESARLTNPLGFNVTSYRVDPE 234
               SCOP domains d4akze_ E: Type IV secretion system protein VirB8                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh...eeeeeeeeeeee....eeeeeeeeeeee.----..eeeeeeeeeeeee.hhhhhhhhhhh.....eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4akz E  97 SYDTVMDKYWLSQYVIARETYDWYTLQKDYETVGMLSSPSEGQSYASQFQGDKALDKQYGSNVRTSVTIVSIVPNGKGIGTVRFAKTTKRT----DGETTHWIATIGYQYVNPSLMSESARLTNPLGFNVTSYRVDPE 234
                                   106       116       126       136       146       156       166       176       186|    | 196       206       216       226        
                                                                                                                    187  192
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 5)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E   (VIRB8_BRUSU | Q7CEG3)
molecular function
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
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.
    GO:0030255    protein secretion by the type IV secretion system    The process in which proteins are transferred into the extracellular milieu or directly into host cells, via the type IV protein secretion system.
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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  4akz
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 Related Entries

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

UniProtKB/Swiss-Prot
        VIRB8_BRUSU | Q7CEG3: 2bhm 4aky 5jbs

(-) Related Entries Specified in the PDB File

2bhm CRYSTAL STRUCTURE OF VIRB8 FROM BRUCELLA SUIS
4aky CRYSTAL STRUCTURE OF VIRB8 FROM BRUCELLA SUIS IN COMPLEX WITH INTERACTION INHIBITOR 2-(BUTYLAMINO)-8- QUINOLINOL