6EY6 | pdb_00006ey6

C-terminal part (residues 315-516) of PorM with the llama nanobody nb130


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.215 (Depositor), 0.213 (DCC) 
  • R-Value Work: 
    0.181 (Depositor) 
  • R-Value Observed: 
    0.182 (Depositor) 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6EY6

This is version 1.4 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: https://doi.org/10.1038/s41467-017-02784-7
  • Primary Citation 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.

Macromolecule Content 

  • Total Structure Weight: 395.46 kDa 
  • Atom Count: 21,404 
  • Modeled Residue Count: 2,645 
  • Deposited Residue Count: 3,624 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
T9SS component cytoplasmic membrane protein PorM
A, B, C, D, E
A, B, C, D, E, F, G, H
315Porphyromonas gingivalisMutation(s): 0 
Gene Names: porMPGIN_15-9_01458
UniProt
Find proteins for B2RLE8 (Porphyromonas gingivalis (strain ATCC 33277 / DSM 20709 / CIP 103683 / JCM 12257 / NCTC 11834 / 2561))
Explore B2RLE8 
Go to UniProtKB:  B2RLE8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB2RLE8
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
nb130
I, J, K, L, M
I, J, K, L, M, N, O, P
138Lama glamaMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.215 (Depositor), 0.213 (DCC) 
  • R-Value Work:  0.181 (Depositor) 
  • R-Value Observed: 0.182 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.245α = 90.24
b = 77.179β = 91.76
c = 156.302γ = 97.16
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing

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
  • Version 1.2: 2018-03-07
    Changes: Structure summary
  • Version 1.3: 2024-01-17
    Changes: Advisory, Data collection, Database references, Refinement description
  • Version 1.4: 2024-10-23
    Changes: Structure summary