7B7J | pdb_00007b7j

EccD5 ubiqutin like domain from Mycobacterium xenopi

• PDB DOI: https://doi.org/10.2210/pdb7B7J/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Mycobacterium xenopi
• Expression System: Mycolicibacterium smegmatis MC2 155
• Mutation(s): No 


• Deposited: 2020-12-10 Released: 2021-07-07 
• Deposition Author(s): Beckham, K.S., Wilmanns, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free: 
  0.216 (Depositor), 0.222 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.183 (Depositor) 

Starting Model: experimental

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

• PubMed: 34172453 
• DOI: https://doi.org/10.1126/sciadv.abg9923
• Primary Citation 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.

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Organizational Affiliation: 
• European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, 22607 Hamburg, Germany.
European Molecular Biology Laboratory, Heidelberg, Germany.
European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, 22607 Hamburg, Germany. [e-mail] [e-mail].
Centre for Structural Systems Biology (CSSB), Hamburg, Germany.
Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
University Hamburg Clinical Centre Hamburg-Eppendorf, Martinistrasse 52, 20246 Hamburg, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 14.02 kDa 
• Atom Count: 742 
• Modeled Residue Count: 91 
• Deposited Residue Count: 129 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Secretion protein Snm4	A	129	Mycobacterium xenopi	Mutation(s): 0  Gene Names: snm, NCTC10042_04572

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free:  0.216 (Depositor), 0.222 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.979	α = 90
b = 43.979	β = 90
c = 85.146	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-07-07 
Deposition Author(s): Beckham, K.S., Wilmanns, M.

Revision History  

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