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(-) Description

Title :  THE STRUCTURE OF YERSINIA PESTIS V-ANTIGEN, AN ESSENTIAL VIRULENCE FACTOR AND MEDIATOR OF IMMUNITY AGAINST PLAGUE
 
Authors :  U. Derewenda, A. Mateja, Y. Devedjiev, K. M. Routzahn, A. G. Evdokimov, Z. S. Derewenda, D. S. Waugh
Date :  15 Oct 03  (Deposition) - 09 Mar 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.17
Chains :  Asym./Biol. Unit :  A
Keywords :  Coiled-Coil, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  U. Derewenda, A. Mateja, Y. Devedjiev, K. M. Routzahn, A. G. Evdokimov, Z. S. Derewenda, D. S. Waugh
The Structure Of Yersinia Pestis V-Antigen, An Essential Virulence Factor And Mediator Of Immunity Against Plague
Structure V. 12 301 2004
PubMed-ID: 14962390  |  Reference-DOI: 10.1016/J.STR.2004.03.008
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - VIRULENCE-ASSOCIATED V ANTIGEN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: MBP-LCRV(DELTA1-23-C273S)-HIS6
    Expression System Strain: BL21(DE3)-RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: LCRV FRAGMENT 24-323
    Mutation: YES
    Organism Scientific: YERSINIA PESTIS
    Organism Taxid: 632
    Synonym: LOW CALCIUM RESPONSE LOCUS PROTEIN V

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1R6F)

(-) Sites  (0, 0)

(no "Site" information available for 1R6F)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1R6F)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1R6F)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1R6F)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1R6F)

(-) Exons   (0, 0)

(no "Exon" information available for 1R6F)

(-) 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:272
 aligned with LCRV_YERPE | P0C7U7 from UniProtKB/Swiss-Prot  Length:326

    Alignment length:295
                                    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     
           LCRV_YERPE    28 GSSVLEELVQLVKDKNIDISIKYDPRKDSEVFANRVITDDIELLKKILAYFLPEDAILKGGHYDNQLQNGIKRVKEFLESSPNTQWELRAFMAVMHFSLTADRIDDDILKVIVDSMNHHGDARSKLREELAELTAELKIYSVIQAEINKHLSSSGTINIHDKSINLMDKNLYGYTDEEIFKASAEYKILEKMPQTTIQVDGSEKKIVSIKDFLGSENKRTGALGNLKNSYSYNKDNNELSHFATTCSDKSRPLNDLVSQKTTQLSDITSRFNSAIEALNRFIQKYDSVMQRLLDD 322
               SCOP domains d1r6fa_ A: Low calcium            response locus protein V, Lc rV                                                                                                                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains LcrV-1r6fA01 A:28-322                                                                                                                                                                                                                                                                                   Pfam domains
         Sec.struct. author .................eee..-----------......hhhhhhhhhhhhhhhhhh.....-hhhhhhhhhhhhhhhhhh...eeehhhhhhhhhhhhh....hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheee.........hhhhh...hhhhhhhhhhhhhhh....eeee....eeee.hhhhhhh..............eee....-----------.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1r6f A  28 GSSVLEELVQLVAAANIDISIK-----------NRVITDDIELLKKILAYFLPEDAILKGGH-DNQLQNGIKRVKEFLESSPNTQWELRAFMAVMHFSLTADRIDDDILKVIVDSMNHHGDARSKLREELAELTAELKIYSVIQAEINKHLSSSGTINIHDKSINLMDKNLYGYTDEEIFKASAEYKILEKMPQTTIQVDGSEKKIVSIKDFLGSENKRTGALGNLKNSYSYNKD-----------SDKSRPLNDLVSQKTTQLSDITSRFNSAIEALNRFIQKYDSVMQRLLDD 322
                                    37        47 |       -   |    67        77        87 | |    97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257    |    -      |277       287       297       307       317     
                                                49          61                          89 |                                                                                                                                                                        262         274                                                
                                                                                          91                                                                                                                                                                                                                                       


Chain A from PDB  Type:PROTEIN  Length:272
 aligned with LCRV_YERPG | A9R9H4 from UniProtKB/Swiss-Prot  Length:326

    Alignment length:295
                                    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     
           LCRV_YERPG    28 GSSVLEELVQLVKDKNIDISIKYDPRKDSEVFANRVITDDIELLRKILAYFLPEDAILKGGHYDNQLQNGIKRVKEFLESSPNTQWELRAFMAVMHFSLTADRIDDDILKVIVDSMNHHGDARSKLREELAELTAELKIYSVIQAEINKHLSSSGTINIHDKSINLMDKNLYGYTDEEIFKASAEYKILEKMPQTTIQVDGSEKKIVSIKDFLGSENKRTGALGNLKNSYSYNKDNNELSHFATTSSDKSRPLNDLVSQKTTQLSDITSRFNSAIEALNRFIQKYDSVMQRLLDD 322
               SCOP domains d1r6fa_ A: Low calcium            response locus protein V, Lc rV                                                                                                                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains LcrV-1r6fA01 A:28-322                                                                                                                                                                                                                                                                                   Pfam domains
         Sec.struct. author .................eee..-----------......hhhhhhhhhhhhhhhhhh.....-hhhhhhhhhhhhhhhhhh...eeehhhhhhhhhhhhh....hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheee.........hhhhh...hhhhhhhhhhhhhhh....eeee....eeee.hhhhhhh..............eee....-----------.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1r6f A  28 GSSVLEELVQLVAAANIDISIK-----------NRVITDDIELLKKILAYFLPEDAILKGGH-DNQLQNGIKRVKEFLESSPNTQWELRAFMAVMHFSLTADRIDDDILKVIVDSMNHHGDARSKLREELAELTAELKIYSVIQAEINKHLSSSGTINIHDKSINLMDKNLYGYTDEEIFKASAEYKILEKMPQTTIQVDGSEKKIVSIKDFLGSENKRTGALGNLKNSYSYNKD-----------SDKSRPLNDLVSQKTTQLSDITSRFNSAIEALNRFIQKYDSVMQRLLDD 322
                                    37        47 |       -   |    67        77        87 | |    97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257    |    -      |277       287       297       307       317     
                                                49          61                          89 |                                                                                                                                                                        262         274                                                
                                                                                          91                                                                                                                                                                                                                                       


Chain A from PDB  Type:PROTEIN  Length:272
 aligned with LCRV_YERPP | A4TSQ1 from UniProtKB/Swiss-Prot  Length:324

    Alignment length:295
                                    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     
           LCRV_YERPP    28 GSSVLEELVQLVKDKNIDISIKYDPRKDSEVFANRVITDDIELLKKILAYFLPEDAILKGGHYDNQLQNGIKRVKEFLESSPNTQWELRAFMAVMHFSLTADRIDDDILKVIVDSMNHHGDARSKLREELAELTAELKIYSVIQAEINKHLSSSGTINIHDKSINLMDKNLYGYTDEEIFKASAEYKILEKMPQTTIQVDGSEKKIVSIKDFLGSENKRTGALGNLKNSYSYNKDNNELSHFATTCSDKSRPLNDLVSQKTTQLSDITSRFNSAIEALNRFIQKYDSVMQRLLDD 322
               SCOP domains d1r6fa_ A: Low calcium            response locus protein V, Lc rV                                                                                                                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains LcrV-1r6fA01 A:28-322                                                                                                                                                                                                                                                                                   Pfam domains
         Sec.struct. author .................eee..-----------......hhhhhhhhhhhhhhhhhh.....-hhhhhhhhhhhhhhhhhh...eeehhhhhhhhhhhhh....hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheee.........hhhhh...hhhhhhhhhhhhhhh....eeee....eeee.hhhhhhh..............eee....-----------.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1r6f A  28 GSSVLEELVQLVAAANIDISIK-----------NRVITDDIELLKKILAYFLPEDAILKGGH-DNQLQNGIKRVKEFLESSPNTQWELRAFMAVMHFSLTADRIDDDILKVIVDSMNHHGDARSKLREELAELTAELKIYSVIQAEINKHLSSSGTINIHDKSINLMDKNLYGYTDEEIFKASAEYKILEKMPQTTIQVDGSEKKIVSIKDFLGSENKRTGALGNLKNSYSYNKD-----------SDKSRPLNDLVSQKTTQLSDITSRFNSAIEALNRFIQKYDSVMQRLLDD 322
                                    37        47 |       -   |    67        77        87 | |    97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257    |    -      |277       287       297       307       317     
                                                49          61                          89 |                                                                                                                                                                        262         274                                                
                                                                                          91
   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, 1)

Asymmetric/Biological Unit
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1R6F)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: LcrV] (1)

(-) Gene Ontology  (2, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (LCRV_YERPG | A9R9H4)
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   (LCRV_YERPE | P0C7U7)
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   (LCRV_YERPP | A4TSQ1)
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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 Related Entries

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

UniProtKB/Swiss-Prot
        LCRV_YERPE | P0C7U7: 4jbu

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1R6F)