4YVM

X-ray structure of Helicobacter pylori CagL-K74


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.79 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of CagL from Helicobacter pylori K74 strain.

Choi, J.M.Choi, Y.H.Sudhanva, M.S.Devakumar, S.Lee, K.H.Cha, J.H.Lee, S.H.

(2015) Biochem Biophys Res Commun 460: 964-970

  • DOI: https://doi.org/10.1016/j.bbrc.2015.03.135
  • Primary Citation of Related Structures:  
    4YVM

  • PubMed Abstract: 

    Helicobacter pylori (Hp) CagL is a component of the type IV secretion system (T4SS) and interacts with integrin in host cells through its flexible RGD domain to translocate CagA. Differences in CagL amino acid polymorphisms between Western and East-Asian Hps are correlated with clinical outcome. CagL of East-Asian clinical Hp isolate K74 (CagL(K74)) contains multiple residue variations upstream of RGD motif and has different integrin binding affinities compared to those of CagL from Western Hp 26695. Here, we report the crystal structure of CagL(K74). The structure displayed a six-helix bundle including two short α-helices, and the RGD motif was found in the long rigid α2 helix flanked by the conserved protease-sensitive and RGD-helper sequences, as observed in CagL(26695). However, two additional salt bridges were found between the helices compared with the CagL(26695) structure, suggesting that the putative flexible region harboring the RGD motif may be more stable in this CagL variant.


  • Organizational Affiliation

    Department of Cellular and Molecular Medicine, Chosun University School of Medicine, Gwangju 501-759, Republic of Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cag pathogenicity island protein
A, B
221Helicobacter pyloriMutation(s): 0 
Gene Names: HP0539
UniProt
Find proteins for Q75XL3 (Helicobacter pylori)
Explore Q75XL3 
Go to UniProtKB:  Q75XL3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ75XL3
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.79 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.616α = 90
b = 97.616β = 90
c = 144.242γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data collection
HKL-2000data scaling
HKL-2000data processing
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (NRF)Korea, Republic Of2013R1A12057465
National Research Foundation (NRF)Korea, Republic Of2012R1A1A2008554

Revision History  (Full details and data files)

  • Version 1.0: 2015-05-13
    Type: Initial release
  • Version 1.1: 2015-05-20
    Changes: Database references
  • Version 1.2: 2024-04-03
    Changes: Data collection, Database references, Derived calculations, Refinement description, Source and taxonomy