9V99 | pdb_00009v99

Crystal structure of the periplasmic domain of CadF from Campylobacter jejuni in complex with a peptidoglycan peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.237 (Depositor), 0.236 (DCC) 
  • R-Value Work: 
    0.207 (Depositor), 0.208 (DCC) 
  • R-Value Observed: 
    0.208 (Depositor) 

Starting Model: in silico
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 9V99

Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history

Literature

Crystal structures of Campylobacter jejuni CadF reveal a potential role for the arginine residue R268 in peptidoglycan recognition and pocket formation.

Oh, H.B.Yoon, S.I.

(2025) Sci Rep 15: 36733-36733

  • DOI: https://doi.org/10.1038/s41598-025-20604-7
  • Primary Citation Related Structures: 
    9V99, 9V9A, 9V9B

  • PubMed Abstract: 

    Campylobacter jejuni is a pathogenic gram-negative bacterium that primarily causes foodborne enteritis in humans. The C. jejuni protein CadF is located in the outer membrane and is essential for the adhesion of C. jejuni to human cells. CadF contains an outer membrane-embedded domain and a periplasmic domain (CadF PD ). The transmembrane domain is well known to bind fibronectin, contributing to host cell recognition. However, the exact function of the CadF PD has never been assessed experimentally. In this study, we present the crystal structures of the CadF PD and demonstrate that CadF may function as a peptidoglycan-binding protein. The CadF PD adopts a two-layer α/β structure and harbors a narrow pocket. The CadF PD interacts with a peptidoglycan-derived peptide by accommodating m-diaminopimelic acid (m-DAP), a non-proteinogenic amino acid of the gram-negative peptidoglycan peptide, into the pocket. The positively charged R268 residue of CadF forms the base of the pocket and specifically interacts with the carboxyl group of m-DAP via salt bridges. This observation combined with the ligand-less structure of the CadF PD mutant R268E highlights the potential role of the R268 residue in maintaining the intact pocket in the CadF PD structure and mediating peptidoglycan recognition.


  • Organizational Affiliation
    • Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon, 24341, Republic of Korea.

Macromolecule Content 

  • Total Structure Weight: 27.38 kDa 
  • Atom Count: 1,932 
  • Modeled Residue Count: 231 
  • Deposited Residue Count: 239 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Outer membrane beta-barrel domain-containing protein
A, B
118Campylobacter jejuniMutation(s): 0 
Gene Names: C3H42_04770C3H48_01715C3H57_06665
UniProt
Find proteins for A0A1E7NJR0 (Campylobacter jejuni)
Explore A0A1E7NJR0 
Go to UniProtKB:  A0A1E7NJR0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1E7NJR0
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
API-DAL-DALC [auth I]3Escherichia coliMutation(s): 0 

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
API

Query on API



Download:Ideal Coordinates CCD File
D [auth B]2,6-DIAMINOPIMELIC ACID
C7 H14 N2 O4
GMKMEZVLHJARHF-SYDPRGILSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
API
Query on API
C [auth I]L-PEPTIDE LINKINGC7 H14 N2 O4LYS
DAL
Query on DAL
C [auth I]D-PEPTIDE LINKINGC3 H7 N O2

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.237 (Depositor), 0.236 (DCC) 
  • R-Value Work:  0.207 (Depositor), 0.208 (DCC) 
  • R-Value Observed: 0.208 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.855α = 90
b = 49.226β = 112.062
c = 55.981γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Korea)Korea, Republic OfRS-2023-00208153

Revision History  (Full details and data files)

  • Version 1.0: 2026-05-06
    Type: Initial release