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(-) Description

Title :  PERIPLASMIC DOMAIN OF THE T3SS INNER MEMBRANE PROTEIN PRGH FROM S.TYPHIMURIUM (FRAGMENT 170-362)
 
Authors :  C. K. Yip, M. Vockovic, A. C. Yu, N. C. J. Strynadka
Date :  24 Mar 09  (Deposition) - 19 May 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Type Iii Secretion System, Inner Membrane Protein, Cell Membrane, Membrane, Transmembrane, Virulence, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Spreter, C. K. Yip, S. Sanowar, I. Andre, T. G. Kimbrough, M. Vuckovic, R. A. Pfuetzner, W. Deng, A. C. Yu, B. B. Finlay, D. Baker, S. I. Miller, N. C. Strynadka
A Conserved Structural Motif Mediates Formation Of The Periplasmic Rings In The Type Iii Secretion System.
Nat. Struct. Mol. Biol. V. 16 468 2009
PubMed-ID: 19396170  |  Reference-DOI: 10.1038/NSMB.1603

(-) Compounds

Molecule 1 - PROTEIN PRGH
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: PRGH PERIPLASMIC DOMAIN, RESIDUES 170-362
    Gene: PRGH, STM2874
    Organism Scientific: SALMONELLA TYPHIMURIUM
    Organism Taxid: 602

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3GR0)

(-) Sites  (0, 0)

(no "Site" information available for 3GR0)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3GR0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3GR0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3GR0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3GR0)

(-) Exons   (0, 0)

(no "Exon" information available for 3GR0)

(-) 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:186
 aligned with PRGH_SALTY | P41783 from UniProtKB/Swiss-Prot  Length:392

    Alignment length:186
                                   186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356      
           PRGH_SALTY   177 LGQEKERFQVLPGRDKMLYVAAQNERDTLWARQVLARGDYDKNARVINENEENKRISIWLDTYYPQLAYYRIHFDEPRKPVFWLSRQRNTMSKKELEVLSQKLRALMPYADSVNITLMDDVTAAGQAEAGLKQQALPYSRRNHKGGVTFVIQGALDDVEILRARQFVDSYYRTWGGRYVQFAIELK 362
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhh...eeee.....eeee..hhhhhhhhhhhhhhhh....eeeehhhhhhhhhhhhhhhhh....eeeee.......eeeee......hhhhhhhhhhhhhhhh......eeeeehhhhhhhhhhhhhhhh...eeeeee..eeeeee....hhhhhhhhhhhhhhhhhhhh...eeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3gr0 A 177 LGQEKERFQVLPGRDKMLYVAAQNERDTLWARQVLARGDYDKNARVINENEENKRISIWLDTYYPQLAYYRIHFDEPRKPVFWLSRQRNTMSKKELEVLSQKLRALMPYADSVNITLMDDVTAAGQAEAGLKQQALPYSRRNHKGGVTFVIQGALDDVEILRARQFVDSYYRTWGGRYVQFAIELK 362
                                   186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356      


Chain B from PDB  Type:PROTEIN  Length:192
 aligned with PRGH_SALTY | P41783 from UniProtKB/Swiss-Prot  Length:392

    Alignment length:192
                                   180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360  
           PRGH_SALTY   171 AELDSLLGQEKERFQVLPGRDKMLYVAAQNERDTLWARQVLARGDYDKNARVINENEENKRISIWLDTYYPQLAYYRIHFDEPRKPVFWLSRQRNTMSKKELEVLSQKLRALMPYADSVNITLMDDVTAAGQAEAGLKQQALPYSRRNHKGGVTFVIQGALDDVEILRARQFVDSYYRTWGGRYVQFAIELK 362
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......hhhhh...eeee.....eeee..hhhhhhhhhhhhhhh.....eeeehhhhhhhhhhhhhhhhh....eeeee.......eeeee......hhhhhhhhhhhhhhhh......eeeeehhhhhhhhhhhhhhhh...eeeeee..eeeeee....hhhhhhhhhhhhhhhhhhhh...eeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3gr0 B 171 AELDSLLGQEKERFQVLPGRDKMLYVAAQNERDTLWARQVLARGDYDKNARVINENEENKRISIWLDTYYPQLAYYRIHFDEPRKPVFWLSRQRNTMSKKELEVLSQKLRALMPYADSVNITLMDDVTAAGQAEAGLKQQALPYSRRNHKGGVTFVIQGALDDVEILRARQFVDSYYRTWGGRYVQFAIELK 362
                                   180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360  


Chain C from PDB  Type:PROTEIN  Length:176
 aligned with PRGH_SALTY | P41783 from UniProtKB/Swiss-Prot  Length:392

    Alignment length:180
                                   192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362
           PRGH_SALTY   183 RFQVLPGRDKMLYVAAQNERDTLWARQVLARGDYDKNARVINENEENKRISIWLDTYYPQLAYYRIHFDEPRKPVFWLSRQRNTMSKKELEVLSQKLRALMPYADSVNITLMDDVTAAGQAEAGLKQQALPYSRRNHKGGVTFVIQGALDDVEILRARQFVDSYYRTWGGRYVQFAIELK 362
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee.....eeee..hhhhhhhhhhhhhh----..eeeehhhhhhhhhhhhhhhhh....eeeee.......eeeee......hhhhhhhhhhhhhhhh......eeeeehhhhhhhhhhhhhhhh...eeeeee..eeeeee....hhhhhhhhhhhhhhhhhhhh...eeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3gr0 C 183 RFQVLPGRDKMLYVAAQNERDTLWARQVLAR----KNARVINENEENKRISIWLDTYYPQLAYYRIHFDEPRKPVFWLSRQRNTMSKKELEVLSQKLRALMPYADSVNITLMDDVTAAGQAEAGLKQQALPYSRRNHKGGVTFVIQGALDDVEILRARQFVDSYYRTWGGRYVQFAIELK 362
                                   192       202       212|    | 222       232       242       252       262       272       282       292       302       312       322       332       342       352       362
                                                        213  218                                                                                                                                                


Chain D from PDB  Type:PROTEIN  Length:180
 aligned with PRGH_SALTY | P41783 from UniProtKB/Swiss-Prot  Length:392

    Alignment length:180
                                   192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362
           PRGH_SALTY   183 RFQVLPGRDKMLYVAAQNERDTLWARQVLARGDYDKNARVINENEENKRISIWLDTYYPQLAYYRIHFDEPRKPVFWLSRQRNTMSKKELEVLSQKLRALMPYADSVNITLMDDVTAAGQAEAGLKQQALPYSRRNHKGGVTFVIQGALDDVEILRARQFVDSYYRTWGGRYVQFAIELK 362
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee.....eeeee.hhhhhhhhhhhhhh......eeeehhhhhhhhhhhhhhhhh....eeeee.......eeeee......hhhhhhhhhhhhhhhh......eeeeehhhhhhhhhhhhhhhh...eeeeee..eeeeee....hhhhhhhhhhhhhhhhhhhh...eeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3gr0 D 183 RFQVLPGRDKMLYVAAQNERDTLWARQVLARGDYDKNARVINENEENKRISIWLDTYYPQLAYYRIHFDEPRKPVFWLSRQRNTMSKKELEVLSQKLRALMPYADSVNITLMDDVTAAGQAEAGLKQQALPYSRRNHKGGVTFVIQGALDDVEILRARQFVDSYYRTWGGRYVQFAIELK 362
                                   192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362
   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 3GR0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3GR0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3GR0)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (PRGH_SALTY | P41783)
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: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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 Related Entries

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

UniProtKB/Swiss-Prot
        PRGH_SALTY | P41783: 2y9j 3gr1 3j1w 3j1x 3j6d 4g1i 4g2s 5tcp 5tcr

(-) Related Entries Specified in the PDB File

3gr1 PERIPLASMIC DOMAIN OF THE T3SS INNER MEMBRANE PROTEIN PRGH FROM S.TYPHIMURIUM (FRAGMENT 170-392)
3gr5 PERIPLASMIC DOMAIN OF THE OUTER MEMBRANE SECRETIN ESCC FROM ENTEROPATHOGENIC E.COLI (EPEC)