6VHR | pdb_00006vhr

Structure of PE5-PPE4-EspG3 complex from the type VII (ESX-3) secretion system, space group I422


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 
    0.266 (Depositor) 
  • R-Value Work: 
    0.248 (Depositor) 
  • R-Value Observed: 
    0.248 (Depositor) 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

PE5-PPE4-EspG3heterotrimer structure from mycobacterial ESX-3 secretion system gives insight into cognate substrate recognition by ESX systems.

Williamson, Z.A.Chaton, C.T.Ciocca, W.A.Korotkova, N.Korotkov, K.V.

(2020) J Biological Chem 295: 12706-12715

  • DOI: https://doi.org/10.1074/jbc.RA120.012698
  • Primary Citation Related Structures: 
    6UUJ, 6VHR

  • PubMed Abstract: 

    Mycobacterium tuberculosis has evolved numerous type VII secretion (ESX) systems to secrete multiple factors important for both growth and virulence across their cell envelope. ESX-1, ESX-3, and ESX-5 systems have been shown to each secrete a distinct set of substrates, including PE and PPE families of proteins, named for conserved Pro-Glu and Pro-Pro-Glu motifs in their N termini. Proper secretion of the PE-PPE proteins requires the presence of EspG, with each system encoding its own unique copy. There is no cross-talk between any of the ESX systems, and how each EspG recognizes its subset of PE-PPE proteins is currently unknown. The only current structural characterization of PE-PPE-EspG heterotrimers is from the ESX-5 system. Here we present the crystal structure of the PE5 mt -PPE4 mt -EspG 3mm heterotrimer from the ESX-3 system. Our heterotrimer reveals that EspG 3mm interacts exclusively with PPE4 mt in a similar manner to EspG 5 , shielding the hydrophobic tip of PPE4 mt from solvent. The C-terminal helical domain of EspG 3mm is dynamic, alternating between "open" and "closed" forms, and this movement is likely functionally relevant in the unloading of PE-PPE heterodimers at the secretion machinery. In contrast to the previously solved ESX-5 heterotrimers, the PE-PPE heterodimer of our ESX-3 heterotrimer is interacting with its chaperone at a drastically different angle and presents different faces of the PPE protein to the chaperone. We conclude that the PPE-EspG interface from each ESX system has a unique shape complementarity that allows each EspG to discriminate among noncognate PE-PPE pairs.


  • Organizational Affiliation
    • Department of Molecular & Cellular Biochemistry and the Center for Structural Biology, University of Kentucky, Lexington, Kentucky, USA.

Macromolecule Content 

  • Total Structure Weight: 58.2 kDa 
  • Atom Count: 3,643 
  • Modeled Residue Count: 497 
  • Deposited Residue Count: 566 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
PE family immunomodulator PE5100Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: PE5Rv0285LH57_01560
UniProt
Find proteins for L7N695 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore L7N695 
Go to UniProtKB:  L7N695
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupL7N695
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
PPE family protein PPE4178Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: PPE4Rv0286
UniProt
Find proteins for P9WI43 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WI43 
Go to UniProtKB:  P9WI43
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WI43
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
ESX-3 secretion-associated protein EspG3288Mycobacterium marinum MMutation(s): 0 
Gene Names: MMAR_0548
UniProt
Find proteins for B2HNX0 (Mycobacterium marinum (strain ATCC BAA-535 / M))
Explore B2HNX0 
Go to UniProtKB:  B2HNX0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB2HNX0
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free:  0.266 (Depositor) 
  • R-Value Work:  0.248 (Depositor) 
  • R-Value Observed: 0.248 (Depositor) 
Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 219.09α = 90
b = 219.09β = 90
c = 104.43γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI119022
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP20GM103486
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP30GM110787

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-29
    Type: Initial release
  • Version 1.1: 2020-09-23
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description