7VEP | pdb_00007vep

Crystal structure and biophysical characterization of TPR domain of EccA5 from ESX-5 pathway of Mycobacterium tuberculosis H37RVR

• PDB DOI: https://doi.org/10.2210/pdb7VEP/pdb

• Classification: HYDROLASE
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-09-09 Released: 2022-09-14 
• Deposition Author(s): Ramachandran, R., Sharma, V.K., Vishwakarma, J.
• Funding Organization(s): Council of Scientific & Industrial Research (CSIR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.216 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Literature

The crystal structure of the TPR domain of the EccA5 ATPase and demonstration of its interaction with EspG5 from the mycobacterial ESX-5 pathway.

Sharma, V.K., Vishwakarma, J., Kabrambam, R., Kumar, S., Ramachandran, R.

(2026) FEBS Lett 

• PubMed: 41761896 
• DOI: https://doi.org/10.1002/1873-3468.70315
• Primary Citation Related Structures: 
  7VEP


• PubMed Abstract: 
  

  The ESX-5 secretion system in Mycobacterium tuberculosis exports PE/PPE virulence factors, with EccA5, an AAA+ ATPase, playing a pivotal role. We solved the crystal structure of EccA5's N-terminal TPR domain (EccA5NT) at 2.15 Å, revealing a monomeric fold with six TPR motifs and a variable β-finger. Biophysical studies, including SAXS and size exclusion chromatography, confirm its monomeric state. A flexible loop (residues 137-148) suggests dynamic substrate interactions. SPR, SAXS and in silico docking show moderate binding (K _D  = 3.43 μm) between EccA5NT's β-finger and EspG5's β2-β3 loop, indicating a role in PE/PPE-EspG5 complex disassembly. These findings elucidate the role of EccA5 in ESX-5-mediated secretion.

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Organizational Affiliation: 
• Biochemistry and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, India.
Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India.

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: 31.4 kDa 
• Atom Count: 2,283 
• Modeled Residue Count: 274 
• Deposited Residue Count: 281 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ESX-5 secretion system protein EccA5	A	281	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: eccA5, Rv1798, MTV049.20
UniProt
Find proteins for P9WPI1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WPI1  Go to UniProtKB:  P9WPI1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4 (Subject of Investigation/LOI)	B [auth A], C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL (Subject of Investigation/LOI)	E [auth A], F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.216 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.236	α = 90
b = 65.645	β = 90
c = 98.204	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-09-14 
Deposition Author(s): Ramachandran, R., Sharma, V.K., Vishwakarma, J.

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Funding Organization	Location	Grant Number
Council of Scientific & Industrial Research (CSIR)	India	--

Revision History  

• Version 1.0: 2022-09-14
  Type: Initial release
  
• Version 1.1: 2024-05-29
  Changes: Data collection
• Version 1.2: 2026-03-18
  Changes: Database references, Structure summary