4KV2 | pdb_00004kv2

Ubiquitin-like domain of the mycobacterium tuberculosis type VII secretion system protein ECCD1

• PDB DOI: https://doi.org/10.2210/pdb4KV2/pdb

• Classification: PROTEIN TRANSPORT
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-05-22 Released: 2014-04-09 
• Deposition Author(s): Korotkov, K.V., Evans, T.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free: 
  0.236 (Depositor), 0.229 (DCC) 
• R-Value Work: 
  0.188 (Depositor) 
• R-Value Observed: 
  0.190 (Depositor) 

Starting Model: experimental

Literature

Structures of EccB1 and EccD1 from the core complex of the mycobacterial ESX-1 type VII secretion system.

Wagner, J.M., Chan, S., Evans, T.J., Kahng, S., Kim, J., Arbing, M.A., Eisenberg, D., Korotkov, K.V.

(2016) BMC Struct Biol 16: 5-5

• PubMed: 26922638 
• DOI: https://doi.org/10.1186/s12900-016-0056-6
• Primary Citation Related Structures: 
  4KK7, 4KV2, 4KV3, 5CYU


• PubMed Abstract: 
  

  The ESX-1 type VII secretion system is an important determinant of virulence in pathogenic mycobacteria, including Mycobacterium tuberculosis. This complicated molecular machine secretes folded proteins through the mycobacterial cell envelope to subvert the host immune response. Despite its important role in disease very little is known about the molecular architecture of the ESX-1 secretion system. This study characterizes the structures of the soluble domains of two conserved core ESX-1 components - EccB1 and EccD1. The periplasmic domain of EccB1 consists of 4 repeat domains and a central domain, which together form a quasi 2-fold symmetrical structure. The repeat domains of EccB1 are structurally similar to a known peptidoglycan binding protein suggesting a role in anchoring the ESX-1 system within the periplasmic space. The cytoplasmic domain of EccD1has a ubiquitin-like fold and forms a dimer with a negatively charged groove. These structures represent a major step towards resolving the molecular architecture of the entire ESX-1 assembly and may contribute to ESX-1 targeted tuberculosis intervention strategies.

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Organizational Affiliation: 
• Department of Molecular & Cellular Biochemistry and Center for Structural Biology, University of Kentucky, 741 South Limestone, Lexington, KY, 40536, USA. [e-mail].
Present address: Department of Molecular Physiology and Biological Physics and The Myles H. Thaler Center for AIDS and Human Retrovirus Research, University of Virginia, Charlottesville, VA, USA. [e-mail].
UCLA-DOE Institute, University of California Los Angeles, Los Angeles, CA, 90095-1570, USA. [e-mail].
Department of Molecular & Cellular Biochemistry and Center for Structural Biology, University of Kentucky, 741 South Limestone, Lexington, KY, 40536, USA. [e-mail].
Present address: Division of Regulatory Services, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, USA. [e-mail].
UCLA-DOE Institute, University of California Los Angeles, Los Angeles, CA, 90095-1570, USA. [e-mail].
UCLA-DOE Institute, University of California Los Angeles, Los Angeles, CA, 90095-1570, USA. [e-mail].
UCLA-DOE Institute, University of California Los Angeles, Los Angeles, CA, 90095-1570, USA. [e-mail].
UCLA-DOE Institute, Departments of Biological Chemistry and Chemistry & Biochemistry, and Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles, CA, 90095-1570, USA. [e-mail].
Department of Molecular & Cellular Biochemistry and Center for Structural Biology, University of Kentucky, 741 South Limestone, Lexington, KY, 40536, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 19.25 kDa 
• Atom Count: 1,526 
• Modeled Residue Count: 180 
• Deposited Residue Count: 184 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ESX-1 secretion system protein eccD1	A, B	92	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: Rv3877, RVBD_3877
UniProt
Find proteins for P9WNQ7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WNQ7  Go to UniProtKB:  P9WNQ7

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free:  0.236 (Depositor), 0.229 (DCC) 
• R-Value Work:  0.188 (Depositor) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.72	α = 90
b = 46.72	β = 90
c = 279.02	γ = 120

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SERGUI	data collection
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-04-09 
Deposition Author(s): Korotkov, K.V., Evans, T.J.

Revision History  

• Version 1.0: 2014-04-09
  Type: Initial release
  
• Version 1.1: 2016-03-23
  Changes: Database references
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Refinement description