2PT7 | pdb_00002pt7

Crystal structure of Cag VirB11 (HP0525) and an inhibitory protein (HP1451)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.270 (Depositor), 0.268 (DCC) 
  • R-Value Work: 
    0.230 (Depositor), 0.229 (DCC) 
  • R-Value Observed: 
    0.232 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Identification, structure and mode of action of a new regulator of the Helicobacter pylori HP0525 ATPase.

Hare, S.Fischer, W.Williams, R.Terradot, L.Bayliss, R.Haas, R.Waksman, G.

(2007) EMBO J 26: 4926-4934

  • DOI: https://doi.org/10.1038/sj.emboj.7601904
  • Primary Citation Related Structures: 
    2PT7

  • PubMed Abstract: 

    Helicobacter pylori is one of the world's most successful human pathogens causing gastric ulcers and cancers. A key virulence factor of H. pylori is the Cag pathogenicity island, which encodes a type IV secretion system. HP0525 is an essential component of the Cag system and acts as an inner membrane associated ATPase. HP0525 forms double hexameric ring structures, with the C-terminal domains (CTDs) forming a closed ring and the N-terminal domains (NTDs) forming a dynamic, open ring. Here, the crystal structure of HP0525 in complex with a fragment of HP1451, a protein of previously unknown function, is reported. The HP1451 construct consists of two domains similar to nucleic acid-binding domains. Two HP1451 molecules bind to the HP0525 NTDs on opposite sides of the hexamer, locking it in the closed form and forming a partial lid over the HP0525 chamber. From the structure, it is suggested that HP1451 acts as an inhibitory factor of HP0525 to regulate Cag-mediated secretion, a suggestion confirmed by results of in vitro ATPase assay and in vivo pull-down experiments.


  • Organizational Affiliation
    • School of Crystallography, Birkbeck College, London, UK.

Macromolecule Content 

  • Total Structure Weight: 260.95 kDa 
  • Atom Count: 17,894 
  • Modeled Residue Count: 2,166 
  • Deposited Residue Count: 2,284 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cag-alfa
A, B, C, D, E
A, B, C, D, E, F
330Helicobacter pylori 26695Mutation(s): 0 
Gene Names: cag-alfacag-alpha
UniProt
Find proteins for Q7BK04 (Helicobacter pylori)
Explore Q7BK04 
Go to UniProtKB:  Q7BK04
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7BK04
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Hypothetical protein
G, H
152Helicobacter pylori 26695Mutation(s): 0 
Gene Names: HP1451
UniProt
Find proteins for O25990 (Helicobacter pylori (strain ATCC 700392 / 26695))
Explore O25990 
Go to UniProtKB:  O25990
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO25990
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.270 (Depositor), 0.268 (DCC) 
  • R-Value Work:  0.230 (Depositor), 0.229 (DCC) 
  • R-Value Observed: 0.232 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.851α = 111.04
b = 86.9β = 95.98
c = 104.129γ = 104.94
Software Package:
Software NamePurpose
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
MOSFLMdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-11-13
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Source and taxonomy, Version format compliance
  • Version 1.2: 2023-08-30
    Changes: Data collection, Database references, Refinement description