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(-) Description

Title :  CRYSTAL STRUCTURE OF TCPA, A TYPE IV PILIN FROM VIBRIO CHOLERAE EL TOR BIOTYPE
 
Authors :  L. Craig, A. S. Arvai, J. A. Tainer
Date :  09 Jun 09  (Deposition) - 16 Jun 10  (Release) - 11 Aug 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Type Iv Pili, Pilin, Vibrio Cholerae, Toxin-Coregulated Pilus, Microcolonies, Colonization, Virulence Factor, Cell Adhesion (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. S. Lim, D. Ng, Z. Zong, A. S. Arvai, R. K. Taylor, J. A. Tainer, L. Craig
Vibrio Cholerae El Tor Tcpa Crystal Structure And Mechanism For Pilus-Mediated Microcolony Formation.
Mol. Microbiol. V. 77 755 2010
PubMed-ID: 20545841  |  Reference-DOI: 10.1111/J.1365-2958.2010.07244.X

(-) Compounds

Molecule 1 - TOXIN COREGULATED PILIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-15B
    Expression System Strain: ORIGAMI B
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: GLOBULAR DOMAIN, RESIDUES 29-199
    Gene: TCPA
    Organism Scientific: VIBRIO CHOLERAE
    Organism Taxid: 666
    Strain: EL TOR H1
    Synonym: TCPA, TOXIN-COREGULATED PILUS SUBUNIT

 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  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2SO43Ligand/IonSULFATE ION
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2SO41Ligand/IonSULFATE ION
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2SO42Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:71 , THR A:91 , ALA A:92 , HOH A:615 , HOH A:617BINDING SITE FOR RESIDUE GOL A 1000
2AC2SOFTWAREARG A:52 , ASN A:198 , HOH A:436 , HOH A:683 , HOH A:724 , HOH A:725BINDING SITE FOR RESIDUE GOL A 1002
3AC3SOFTWAREHIS A:27 , SER A:30 , ASN A:32 , GLN A:119 , HOH A:622 , HOH A:671 , HOH A:828BINDING SITE FOR RESIDUE SO4 A 1101
4AC4SOFTWAREPHE A:88 , HOH A:493 , THR B:67 , ASN B:71 , ALA B:92BINDING SITE FOR RESIDUE GOL B 1001
5AC5SOFTWAREASN B:32 , PHE B:88 , GLN B:119 , THR B:177 , HOH B:537BINDING SITE FOR RESIDUE SO4 B 1100
6AC6SOFTWARETHR B:116 , GLN B:117 , ALA B:118 , ALA B:190 , HOH B:785 , HOH B:786 , HOH B:793BINDING SITE FOR RESIDUE SO4 B 1102

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:120 -A:186
2B:120 -B:186

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ala A:190 -Pro A:191
2Ala B:190 -Pro B:191

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3HRV)

(-) 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:174
 aligned with TCPA_VIBCH | Q60153 from UniProtKB/Swiss-Prot  Length:224

    Alignment length:174
                                    60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220    
           TCPA_VIBCH    51 RAIDSQNMTKAAQNLNSVQIAMTQTYRSLGNYPATANANAATQLANGLVSLGKVSADEAKNPFTGTAMGIFSFPRNSAANKAFAITVGGLTQAQCKTLVTSVGDMFPFINVKEGAFAAVADLGDFETSVADAATGAGVIKSIAPGSANLNLTNITHVEKLCTGTAPFTVAFGNS 224
               SCOP domains d3hrva_ A: Toxin-coregulated pilus subunit TcpA                                                                                                                                SCOP domains
               CATH domains 3hrvA00 A:26-199 TcpA-like pilin                                                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhh...hhhhhh........eeeeeee..eeeeeeeeeeeeehhhhhhhhhhhhhhhh.eeeeee....hhhhhh.......hhhhh.eeee............hhhhhhhh......eeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3hrv A  26 SHMDSQNMTKAAQNLNSVQIAMTQTYRSLGNYPATANANAATQLANGLVSLGKVSADEAKNPFTGTAMGIFSFPRNSAANKAFAITVGGLTQAQCKTLVTSVGDMFPFINVKEGAFAAVADLGDFETSVADAATGAGVIKSIAPGSANLNLTNITHVEKLCTGTAPFTVAFGNS 199
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195    


Chain B from PDB  Type:PROTEIN  Length:170
 aligned with TCPA_VIBCH | Q60153 from UniProtKB/Swiss-Prot  Length:224

    Alignment length:170
                                    64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224
           TCPA_VIBCH    55 SQNMTKAAQNLNSVQIAMTQTYRSLGNYPATANANAATQLANGLVSLGKVSADEAKNPFTGTAMGIFSFPRNSAANKAFAITVGGLTQAQCKTLVTSVGDMFPFINVKEGAFAAVADLGDFETSVADAATGAGVIKSIAPGSANLNLTNITHVEKLCTGTAPFTVAFGNS 224
               SCOP domains d3hrvb_ B: Toxin-coregulated pilus subunit TcpA                                                                                                                            SCOP domains
               CATH domains 3hrvB00 B:30-199 TcpA-like pilin                                                                                                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhh....hhhhh........eeeeeee..eeeeeeeeeeeeehhhhhhhhhhhhhhhh.eeeeee....hhhhhh.......hhhhh.eeee............hhhhhhhh......eeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hrv B  30 SQNMTKAAQNLNSVQIAMTQTYRSLGNYPATANANAATQLANGLVSLGKVSADEAKNPFTGTAMGIFSFPRNSAANKAFAITVGGLTQAQCKTLVTSVGDMFPFINVKEGAFAAVADLGDFETSVADAATGAGVIKSIAPGSANLNLTNITHVEKLCTGTAPFTVAFGNS 199
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199
   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, 2)

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

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (TCPA_VIBCH | Q60153)
molecular function
    GO:0005198    structural molecule activity    The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
biological process
    GO:0030030    cell projection organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a prolongation or process extending from a cell, e.g. a flagellum or axon.
    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:0015628    protein secretion by the type II secretion system    The process in which proteins are secreted across the outer membrane of Gram-negative bacteria by the type II secretion system. Proteins using this pathway are first translocated across the cytoplasmic membrane via the Sec or Tat pathways.
cellular component
    GO:0043230    extracellular organelle    Organized structure of distinctive morphology and function, occurring outside the cell. Includes, for example, extracellular membrane vesicles (EMVs) and the cellulosomes of anaerobic bacteria and fungi.
    GO:0009289    pilus    A proteinaceous hair-like appendage on the surface of bacteria ranging from 2-8 nm in diameter.

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 Related Entries

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(-) Related Entries Specified in the PDB File

1oqv STRUCTURE OF THE TCPA SUBUNIT FROM THE VIBRIO CHOLERAE CLASSICAL BIOTYPE