6EY0

N-terminal part (residues 30-212) of PorM with the llama nanobody nb01


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 10.1038/s41467-017-02784-7
  • Primary Citation of Related Structures:  

  • 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. gingival ...

    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.


    Related Citations: 
    • Camelid nanobodies used as crystallization chaperones for different constructs of PorM, a component of the type IX secretion system from Porphyromonas gingivalis.
      Duhoo, Y.,Roche, J.,Trinh, T.T.N.,Desmyter, A.,Gaubert, A.,Kellenberger, C.,Cambillau, C.,Roussel, A.,Leone, P.
      (2017) Acta Crystallogr F Struct Biol Commun 73: 286


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
T9SS component cytoplasmic membrane protein PorM
A, B, C, D
197Porphyromonas gingivalis (strain ATCC 33277 / DSM 20709 / CIP 103683 / JCM 12257 / NCTC 11834 / 2561)Gene Names: porM
Find proteins for B2RLE8 (Porphyromonas gingivalis (strain ATCC 33277 / DSM 20709 / CIP 103683 / JCM 12257 / NCTC 11834 / 2561))
Go to UniProtKB:  B2RLE8
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
llama nanobody nb01
E, G, H
134N/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
llama nanobody nb01
F
136N/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.213 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 80.283α = 90.00
b = 99.924β = 93.83
c = 80.291γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
XDSdata reduction
BUSTERrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


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

Revision History 

  • Version 1.0: 2018-02-07
    Type: Initial release
  • Version 1.1: 2018-02-14
    Type: Database references
  • Version 1.2: 2018-03-07
    Type: Source and taxonomy, Structure summary