HBP35 of Porphyromonas gingivalis

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 

wwPDB Validation   3D Report Full Report

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Immunoglobulin-like domains of the cargo proteins are essential for protein stability during secretion by the type IX secretion system.

Sato, K.Kakuda, S.Yukitake, H.Kondo, Y.Shoji, M.Takebe, K.Narita, Y.Naito, M.Nakane, D.Abiko, Y.Hiratsuka, K.Suzuki, M.Nakayama, K.

(2018) Mol Microbiol 110: 64-81

  • DOI: https://doi.org/10.1111/mmi.14083
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The periodontal pathogen Porphyromonas gingivalis secretes many potent virulence factors using the type IX secretion system (T9SS). T9SS cargo proteins that have been structurally determined by X-ray crystallography are composed of a signal peptide, functional domain(s), an immunoglobulin (Ig)-like domain and a C-terminal domain. Role of the Ig-like domains of cargo proteins in the T9SS has not been elucidated. Gingipain proteases, which are cargo proteins of the T9SS, were degraded when their Ig-like domains were lacking or truncated. The degradation was dependent on the activity of a quality control factor, HtrA protease. Another T9SS cargo protein, HBP35, which has a thioredoxin domain as a functional domain, was analyzed by X-ray crystallography, revealing that HBP35 has an Ig-like domain after the thioredoxin domain and that the hydrophobic regions of the thioredoxin domain and the Ig-like domain face each other. HBP35 with substitution of hydrophobic amino acids in the Ig-like domain was degraded depending on HtrA. These results suggest that the Ig-like domain mediates stability of the cargo proteins in the T9SS.

  • Organizational Affiliation

    Department of Microbiology and Oral Infection, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Nagasaki, 852-8588, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
35 kDa hemin binding protein344Porphyromonas gingivalisMutation(s): 0 
Gene Names: HBP35AT291_00855
Find proteins for Q8G962 (Porphyromonas gingivalis)
Explore Q8G962 
Go to UniProtKB:  Q8G962
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8G962
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.016α = 90
b = 58.324β = 90
c = 114.417γ = 90
Software Package:
Software NamePurpose
MOLREPdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-07-25
    Type: Initial release
  • Version 1.1: 2019-02-06
    Changes: Data collection, Database references
  • Version 1.2: 2024-03-27
    Changes: Data collection, Database references