3ZCI

Crystal structure of Helicobacter pylori T4SS protein CagL in a cubic crystal form with a distorted helical conformation of the RGD-motif


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

A Helical Rgd Motif Promoting Cell Adhesion: Crystal Structures of the Helicobacter Pylori Type Iv Secretion System Pilus Protein Cagl

Barden, S.Lange, S.Tegtmeyer, N.Conradi, J.Sewald, N.Backert, S.Niemann, H.H.

(2013) Structure 21: 1931

  • DOI: https://doi.org/10.1016/j.str.2013.08.018
  • Primary Citation of Related Structures:  
    3ZCI, 3ZCJ

  • PubMed Abstract: 

    RGD tripeptide motifs frequently mediate ligand binding to integrins. The type IV secretion system (T4SS) protein CagL of the gastric pathogen Helicobacter pylori also contains an RGD motif. CagL decorates the T4SS pilus and may function as an adhesin for host cells. Whether CagL binds integrins via its RGD motif is under debate. Here, we present crystal structures of CagL revealing an elongated four-helix bundle that appears evolutionarily unrelated to the proposed VirB5 orthologs. The RGD motif is surface-exposed but located within a long α helix. This is unprecedented as previously characterized integrin-binding RGD motifs are located within extended or flexible loops. Yet, adhesion of gastric epithelial cells to CagL was strictly RGD-dependent. Comparison of seven crystallographically independent molecules reveals substantial structural flexibility. Intramolecular disulfide bonds engineered to reduce CagL flexibility resulted in more stable protein, but unable to support cell adhesion. CagL may thus partly unfold during receptor binding.


  • Organizational Affiliation

    Structural Biochemistry, Department of Chemistry, Bielefeld University, 33501 Bielefeld, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CAG PATHOGENICITY ISLAND PROTEIN (CAG18)220Helicobacter pylori 26695Mutation(s): 5 
UniProt
Find proteins for O25272 (Helicobacter pylori (strain ATCC 700392 / 26695))
Explore O25272 
Go to UniProtKB:  O25272
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO25272
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
BU9
Query on BU9

Download Ideal Coordinates CCD File 
G [auth A],
J [auth A],
K [auth A]
Meso-2,3-Butanediol
C4 H10 O2
OWBTYPJTUOEWEK-ZXZARUISSA-N
DIO
Query on DIO

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
H [auth A]
1,4-DIETHYLENE DIOXIDE
C4 H8 O2
RYHBNJHYFVUHQT-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
I [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 
  • Space Group: F 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 181.002α = 90
b = 181.002β = 90
c = 181.002γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
SHELXCDEphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-10-09
    Type: Initial release
  • Version 1.1: 2013-11-27
    Changes: Database references
  • Version 1.2: 2019-03-06
    Changes: Data collection, Derived calculations, Experimental preparation, Other
  • Version 1.3: 2019-09-25
    Changes: Data collection, Experimental preparation, Other
  • Version 1.4: 2024-10-16
    Changes: Data collection, Database references, Derived calculations, Structure summary