7B7J

EccD5 ubiqutin like domain from Mycobacterium xenopi


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure of the mycobacterial ESX-5 type VII secretion system pore complex.

Beckham, K.S.H.Ritter, C.Chojnowski, G.Ziemianowicz, D.S.Mullapudi, E.Rettel, M.Savitski, M.M.Mortensen, S.A.Kosinski, J.Wilmanns, M.

(2021) Sci Adv 7

  • DOI: https://doi.org/10.1126/sciadv.abg9923
  • Primary Citation of Related Structures:  
    7B7J, 7B9F, 7B9S

  • PubMed Abstract: 

    The ESX-5 type VII secretion system is a membrane-spanning protein complex key to the virulence of mycobacterial pathogens. However, the overall architecture of the fully assembled translocation machinery and the composition of the central secretion pore have remained unknown. Here, we present the high-resolution structure of the 2.1-megadalton ESX-5 core complex. Our structure captured a dynamic, secretion-competent conformation of the pore within a well-defined transmembrane section, sandwiched between two flexible protein layers at the cytosolic entrance and the periplasmic exit. We propose that this flexibility endows the ESX-5 machinery with large conformational plasticity required to accommodate targeted protein secretion. Compared to known secretion systems, a highly dynamic state of the pore may represent a fundamental principle of bacterial secretion machineries.


  • Organizational Affiliation

    European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, 22607 Hamburg, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Secretion protein Snm4129Mycobacterium xenopiMutation(s): 0 
Gene Names: snmNCTC10042_04572
Membrane Entity: Yes 
UniProt
Find proteins for I0RSS8 (Mycobacterium xenopi RIVM700367)
Explore I0RSS8 
Go to UniProtKB:  I0RSS8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI0RSS8
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.979α = 90
b = 43.979β = 90
c = 85.146γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-07
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Database references, Refinement description