5NFI | pdb_00005nfi

The fimbrial anchor protein Mfa2 from Porphyromonas gingivalis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 
    0.263 (Depositor), 0.264 (DCC) 
  • R-Value Work: 
    0.197 (Depositor), 0.208 (DCC) 
  • R-Value Observed: 
    0.200 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5NFI

This is version 2.0 of the entry. See complete history

Literature

Structural and functional characterization of shaft, anchor, and tip proteins of the Mfa1 fimbria from the periodontal pathogen Porphyromonas gingivalis.

Hall, M.Hasegawa, Y.Yoshimura, F.Persson, K.

(2018) Sci Rep 8: 1793-1793

  • DOI: https://doi.org/10.1038/s41598-018-20067-z
  • Primary Citation Related Structures: 
    5NF2, 5NF3, 5NF4, 5NFI

  • PubMed Abstract: 

    Very little is known about how fimbriae of Bacteroidetes bacteria are assembled. To shed more light on this process, we solved the crystal structures of the shaft protein Mfa1, the regulatory protein Mfa2, and the tip protein Mfa3 from the periodontal pathogen Porphyromonas gingivalis. Together these build up part of the Mfa1 fimbria and represent three of the five proteins, Mfa1-5, encoded by the mfa1 gene cluster. Mfa1, Mfa2 and Mfa3 have the same overall fold i.e., two β-sandwich domains. Upon polymerization, the first β-strand of the shaft or tip protein is removed by indigenous proteases. Although the resulting void is expected to be filled by a donor-strand from another fimbrial protein, the mechanism by which it does so is still not established. In contrast, the first β-strand in Mfa2, the anchoring protein, is firmly attached by a disulphide bond and is not cleaved. Based on the structural information, we created multiple mutations in P. gingivalis and analysed their effect on fimbrial polymerization and assembly in vivo. Collectively, these data suggest an important role for the C-terminal tail of Mfa1, but not of Mfa3, affecting both polymerization and maturation of downstream fimbrial proteins.


  • Organizational Affiliation
    • Department of Chemistry, Umeå University, Umeå, SE-901 85, Sweden.

Macromolecule Content 

  • Total Structure Weight: 32.21 kDa 
  • Atom Count: 2,242 
  • Modeled Residue Count: 277 
  • Deposited Residue Count: 281 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Minor fimbrium anchoring subunit Mfa2A [auth B]281Porphyromonas gingivalis ATCC 33277Mutation(s): 0 
Gene Names: mfa2PGN_0288
UniProt
Find proteins for B2RHG2 (Porphyromonas gingivalis (strain ATCC 33277 / DSM 20709 / CIP 103683 / JCM 12257 / NCTC 11834 / 2561))
Explore B2RHG2 
Go to UniProtKB:  B2RHG2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB2RHG2
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A [auth B]L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free:  0.263 (Depositor), 0.264 (DCC) 
  • R-Value Work:  0.197 (Depositor), 0.208 (DCC) 
  • R-Value Observed: 0.200 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.6α = 90
b = 83.21β = 94.76
c = 38.74γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
CRANK2phasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Research CouncilSweden2016-05009
Japan Society for the Promotion of ScienceJapan16K11466

Revision History  (Full details and data files)

  • Version 1.0: 2018-02-07
    Type: Initial release
  • Version 2.0: 2024-11-20
    Changes: Atomic model, Data collection, Database references, Structure summary