4F3V

Crystal structure of N-terminal domain of EccA1 ATPase from ESX-1 secretion system of Mycobacterium tuberculosis

• PDB DOI: https://doi.org/10.2210/pdb4F3V/pdb

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


• Deposited: 2012-05-09 Released: 2012-06-06 
• Deposition Author(s): Korotkov, K.V., Evans, T.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.211 
• R-Value Work: 0.174 
• R-Value Observed: 0.176 

Literature

Crystal structure of the N-terminal domain of EccA1 ATPase from the ESX-1 secretion system of Mycobacterium tuberculosis.

Wagner, J.M., Evans, T.J., Korotkov, K.V.

(2014) Proteins 82: 159-163

• PubMed: 23818233 
• DOI: https://doi.org/10.1002/prot.24351
• Primary Citation of Related Structures:  
  4F3V


• PubMed Abstract: 
  

  EccA1 is an important component of the type VII secretion system (T7SS) that is responsible for transport of virulence factors in pathogenic mycobacteria. EccA1 has an N-terminal domain of unknown function and a C-terminal AAA+ (ATPases associated with various cellular activities) domain. Here we report the crystal structure of the N-terminal domain of EccA1 from Mycobacterium tuberculosis, which shows an arrangement of six tetratricopeptide repeats that may mediate interactions of EccA1 with secreted substrates. Furthermore, the size and shape of the N-terminal domain suggest its orientation in the context of a hexamer model of full-length EccA1.

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Organizational Affiliation: 

Department of Molecular and Cellular Biochemistry and Center for Structural Biology, University of Kentucky, Lexington, Kentucky, 40536.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 61.63 kDa 
• Atom Count: 4,621 
• Modelled Residue Count: 548 
• Deposited Residue Count: 564 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ESX-1 secretion system protein EccA1	A, B	282	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names: eccA1, MT3981, MTV027.03, Rv3868
UniProt
Find proteins for P9WPH9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WPH9  Go to UniProtKB:  P9WPH9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SM	C [auth A], H [auth B], I [auth B]	SAMARIUM (III) ION Sm DOSGOCSVHPUUIA-UHFFFAOYSA-N
SO4	D [auth A], E [auth A], F [auth A], G [auth A], J [auth B], K [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.211 
• R-Value Work: 0.174 
• R-Value Observed: 0.176 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.23	α = 90
b = 92.51	β = 90
c = 105.71	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SERGUI	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-06-06 
Deposition Author(s): Korotkov, K.V., Evans, T.J.

Revision History  

• Version 1.0: 2012-06-06
  Type: Initial release
  
• Version 1.1: 2013-07-10
  Changes: Database references
• Version 1.2: 2013-12-25
  Changes: Database references
• Version 1.3: 2024-02-28
  Changes: Data collection, Database references, Derived calculations, Refinement description