Periplasmic domain (residues 36-513) of GldM

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 

wwPDB Validation   3D Report Full Report

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Type IX secretion system PorM and gliding machinery GldM form arches spanning the periplasmic space.

Leone, P.Roche, J.Vincent, M.S.Tran, Q.H.Desmyter, A.Cascales, E.Kellenberger, C.Cambillau, C.Roussel, A.

(2018) Nat Commun 9: 429-429

  • DOI: https://doi.org/10.1038/s41467-017-02784-7
  • Primary Citation of Related Structures:  
    6EY0, 6EY4, 6EY5, 6EY6

  • PubMed Abstract: 

    Type IX secretion system (T9SS), exclusively present in the Bacteroidetes phylum, has been studied mainly in Flavobacterium johnsoniae and Porphyromonas gingivalis. Among the 18 genes, essential for T9SS function, a group of four, porK-N (P. gingivalis) or gldK-N (F. johnsoniae) belongs to a co-transcribed operon that expresses the T9SS core membrane complex. The central component of this complex, PorM (or GldM), is anchored in the inner membrane by a trans-membrane helix and interacts through the outer membrane PorK-N complex. There is a complete lack of available atomic structures for any component of T9SS, including the PorKLMN complex. Here we report the crystal structure of the GldM and PorM periplasmic domains. Dimeric GldM and PorM, each contain four domains of ~180-Å length that span most of the periplasmic space. These and previously reported results allow us to propose a model of the T9SS core membrane complex as well as its functional behavior.

  • Organizational Affiliation

    Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, UMR 7257, 163 Avenue de Luminy, Case 932, 13009, Marseille, France.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GldM501Flavobacterium johnsoniaeMutation(s): 0 
Gene Names: gldM
Find proteins for Q5EGM3 (Flavobacterium johnsoniae)
Explore Q5EGM3 
Go to UniProtKB:  Q5EGM3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5EGM3
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 
  • Space Group: P 64 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.377α = 90
b = 71.377β = 90
c = 426.941γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
French National Research AgencyFranceANR-15-CE11-0019-01
French Infrastructure for Integrated Structural BiologyFrance--

Revision History  (Full details and data files)

  • Version 1.0: 2018-02-07
    Type: Initial release
  • Version 1.1: 2018-02-14
    Changes: Database references