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(-) Description

Title :  PRGI-SIPD FROM SALMONELLA TYPHIMURIUM
 
Authors :  M. Lunelli, M. Kolbe
Date :  08 Jun 11  (Deposition) - 17 Aug 11  (Release) - 28 Mar 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Cell Invasion, Type Iii Secretion, T3Ss, Tip Complex, Host Pathogen Interaction, Bacterial Pathogenesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Lunelli, R. Hurwitz, J. Lambers, M. Kolbe
Crystal Structure Of Prgi-Sipd: Insight Into A Secretion Competent State Of The Type Three Secretion System Needle Tip And Its Interaction With Host Ligands
Plos Pathog. V. 7 02163 2011
PubMed-ID: 21829362  |  Reference-DOI: 10.1371/JOURNAL.PPAT.1002163

(-) Compounds

Molecule 1 - PROTEIN PRGI, CELL INVASION PROTEIN SIPD
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET-28A
    Expression System Vector Type: PLASMID
    Fragment: PRGI FUSED WITH SIPD RESIDUES 127-343
    Organism Scientific: SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM
    Organism Taxid: 216597
    Other Details: GGSGG LINK INSERTED BETWEEN PRGI AND SIPD
    Strain: SL1344
    Synonym: SALMONELLA INVASION PROTEIN D, PRGI-SIPD FUSION PROTEIN

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:249 , ASN A:316 , ASP A:320 , GLN B:288BINDING SITE FOR RESIDUE GOL A1336
2AC2SOFTWARESER A:317 , ASP B:267 , GLY B:293 , ALA B:296 , GLN B:297 , HOH B:2030BINDING SITE FOR RESIDUE GOL B1340
3AC3SOFTWARESER B:200 , ASN B:203BINDING SITE FOR RESIDUE GOL B1341

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3ZQB)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Phe A:215 -Pro A:216
2Phe B:215 -Pro B:216

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3ZQB)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3ZQB)

(-) Exons   (0, 0)

(no "Exon" information available for 3ZQB)

(-) 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:274
 aligned with PRGI_SALTY | P41784 from UniProtKB/Swiss-Prot  Length:80

    Alignment length:274
                                                                                                                                           80                                                                                                                                                                 
                                                                                                   78                                     79|                                                                                                                                                                 
                                    15        25        35        45        55        65        75  |      -         -         -         - ||      -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -    
           PRGI_SALTY     6 SGYLDDVSAKFDTGVDNLQTQVTEALDKLAAKPSDPALLAAYQSKLSEYNLYRNAQSNTVKVFKDIDAAIIQN--------------------------------------FR-----------------------------------------------------------------------------------------------------------------------------------------------------------------   -
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeehhhhhhhhhhhhhhhh.......eee...........hhhhhhhhhhhh..hhh.eeee..eeeee..hhhhhhhhhhhhhhh.......eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zqb A   6 SGYLDDVSAKFDTGVDNLQTQVTEALDKLAAKPSDPALLAAYQSKLSEYNLYRNAQSNTVKVFKDIDAAIIQNISDAEIWDMVSQNISAIGDSYLGVYENVVAVYTDFYQAFSDILSKMGGWLTVKLDVTSLKNDLNSLVNKYNQINSNTVLFPAQSGSGVKVATEAEARQWLSELNLPNSCLKSYGSGYVVTVDLTPLQKMVQDIDGLGAPGKDSKLEMDNAKYQAWQSGFKAQEENMKTTLQTLTQKYSNANSLYDNLVKVLSSTISSSLET 336
                                    15        25        35        45        55        65        75  ||   135       145       155       165       175  ||   192       202       212       222       232       242       252       262       272       282       292       302       312       322       332    
                                                                                                   78|                                              178|                                                                                                                                                      
                                                                                                   129                                               186                                                                                                                                                      


Chain A from PDB  Type:PROTEIN  Length:274
 aligned with SIPD_SALTY | Q56026 from UniProtKB/Swiss-Prot  Length:343

    Alignment length:324
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332    
           SIPD_SALTY    13 PGIVAERPQTPSASEHVETAVVPSTTEHRGTDIISLSQAATKIHQAQQTLQSTPPISEENNDERTLARQQLTSSLNALAKSGVSLSAEQNENLRSAFSAPTSALFSASPMAQPRTTISDAEIWDMVSQNISAIGDSYLGVYENVVAVYTDFYQAFSDILSKMGGWLLPGKDGNTVKLDVTSLKNDLNSLVNKYNQINSNTVLFPAQSGSGVKVATEAEARQWLSELNLPNSCLKSYGSGYVVTVDLTPLQKMVQDIDGLGAPGKDSKLEMDNAKYQAWQSGFKAQEENMKTTLQTLTQKYSNANSLYDNLVKVLSSTISSSLET 336
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhh------hhhhhhhhhh---------------hhhhhhhhhhhhhhhh.------.hhhhhhhhhhhhhhhhhhhh-----hhhh----------hhhhhhhhhhhhh..-.hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh-------.eeehhhhhhhhhhhhhhhh.......eee...........hhhhhhhhhhhh..hhh.eeee..eeeee..hhhhhhhhhhhhhhh.......eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3zqb A   6 SGYLDD------VSAKFDTGVD---------------NLQTQVTEALDKLAAKP------SDPALLAAYQSKLSEYNLYRN-----AQSN----------TVKVFKDIDAAIIQN-ISDAEIWDMVSQNISAIGDSYLGVYENVVAVYTDFYQAFSDILSKMGGWL-------TVKLDVTSLKNDLNSLVNKYNQINSNTVLFPAQSGSGVKVATEAEARQWLSELNLPNSCLKSYGSGYVVTVDLTPLQKMVQDIDGLGAPGKDSKLEMDNAKYQAWQSGFKAQEENMKTTLQTLTQKYSNANSLYDNLVKVLSSTISSSLET 336
                                 |   -  |     19 |       -       |24        34   |     -|       48        58|     | 63         -|       73    | |132       142       152       162       172     |   -   |   192       202       212       222       232       242       252       262       272       282       292       302       312       322       332    
                                11     12       21              22              38     39                  59    60 63         64            78 |                                              178     186                                                                                                                                                      
                                                                                                                                              129                                                                                                                                                                                                               


Chain B from PDB  Type:PROTEIN  Length:264
 aligned with PRGI_SALTY | P41784 from UniProtKB/Swiss-Prot  Length:80

    Alignment length:264
                                                                                          71     72        73     80                                                                                                                                                                                
                                    17        27        37        47        57        67   |     -|        -|      | -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -    
           PRGI_SALTY     8 YLDDVSAKFDTGVDNLQTQVTEALDKLAAKPSDPALLAAYQSKLSEYNLYRNAQSNTVKVFKDI------D---------AAIIQNFR--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eee.hhh.eeeehhhhhhhhhhhhhhhhh......eee...........hhhhhhhhhhhhh.hhh.eeee..eeeee..hhhhhhhhhhhhh.........eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3zqb B   8 YLDDVSAKFDTGVDNLQTQVTEALDKLAAKPSDPALLAAYQSKLSEYNLYRNAQSNTVKVFKDINISAIGDSYLGVYENVVAVYTDFYQAFSDILSKMGGWLLPGKDGNTVKLDVTSLKNDLNSLVNKYNQINSNTVLFPAQSGSGVKVATEAEARQWLSELNLPNSCLKSYGSGYVVTVDLTPLQKMVQDIDGLGAPGKDSKLEMDNAKYQAWQSGFKAQEENMKTTLQTLTQKYSNANSLYDNLVKVLSSTISSSLETAKSF 340
                                    17        27        37        47        57        67   ||  146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336    
                                                                                          71|                                                                                                                                                                                                       
                                                                                          141                                                                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:264
 aligned with SIPD_SALTY | Q56026 from UniProtKB/Swiss-Prot  Length:343

    Alignment length:294
                                    56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336    
           SIPD_SALTY    47 SLSQAATKIHQAQQTLQSTPPISEENNDERTLARQQLTSSLNALAKSGVSLSAEQNENLRSAFSAPTSALFSASPMAQPRTTISDAEIWDMVSQNISAIGDSYLGVYENVVAVYTDFYQAFSDILSKMGGWLLPGKDGNTVKLDVTSLKNDLNSLVNKYNQINSNTVLFPAQSGSGVKVATEAEARQWLSELNLPNSCLKSYGSGYVVTVDLTPLQKMVQDIDGLGAPGKDSKLEMDNAKYQAWQSGFKAQEENMKTTLQTLTQKYSNANSLYDNLVKVLSSTISSSLETAKSF 340
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhh-----------------hhhhhhhhhhhh------..hhhhhhhhhhhhh-hhhhhhhhhhhhhhhhhh.------.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eee.hhh.eeeehhhhhhhhhhhhhhhhh......eee...........hhhhhhhhhhhhh.hhh.eeee..eeeee..hhhhhhhhhhhhh.........eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3zqb B   8 YLDDVSAKFDTGVDNLQT-----------------QVTEALDKLAAK------PSDPALLAAYQSKLS-EYNLYRNAQSNTVKVFKDI------NISAIGDSYLGVYENVVAVYTDFYQAFSDILSKMGGWLLPGKDGNTVKLDVTSLKNDLNSLVNKYNQINSNTVLFPAQSGSGVKVATEAEARQWLSELNLPNSCLKSYGSGYVVTVDLTPLQKMVQDIDGLGAPGKDSKLEMDNAKYQAWQSGFKAQEENMKTTLQTLTQKYSNANSLYDNLVKVLSSTISSSLETAKSF 340
                                    17       | -         -     |  30      |  -   |    44       |53        63       | -    |  146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336    
                                            25                26         37     38            52 |                71    141                                                                                                                                                                                                       
                                                                                                53
   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  (0, 0)

(no "SCOP Domain" information available for 3ZQB)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3ZQB)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3ZQB)

(-) Gene Ontology  (5, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (SIPD_SALTY | Q56026)
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   (PRGI_SALTY | P41784)
molecular function
    GO:0008565    protein transporter activity    Enables the directed movement of proteins into, out of or within a cell, or between cells.
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:0015031    protein transport    The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.

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  3zqb
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  PRGI_SALTY | P41784
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  SIPD_SALTY | Q56026
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 Related Entries

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

UniProtKB/Swiss-Prot
        PRGI_SALTY | P41784: 2jow 2kv7 2lpz 2mex 2x9c 3zqe
        SIPD_SALTY | Q56026: 2ym0 2ym9 3nzz 3o00 3o01 3o02 3zqe

(-) Related Entries Specified in the PDB File

2x9c CRYSTAL STRUCTURE OF A SOLUBLE PRGI MUTANT FROM SALMONELLA TYPHIMURIUM
2ym0 TRUNCATED SIPD FROM SALMONELLA TYPHIMURIUM
2ym9 SIPD FROM SALMONELLA TYPHIMURIUM
3zqe PRGI-SIPD FROM SALMONELLA TYPHIMURIUM IN COMPLEX WITH DEOXYCHOLATE