4FME

EspG-Rab1-Arf6 complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.10 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.208 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Structurally Distinct Bacterial TBC-like GAPs Link Arf GTPase to Rab1 Inactivation to Counteract Host Defenses.

Dong, N., Zhu, Y., Lu, Q., Hu, L., Zheng, Y., Shao, F.

(2012) Cell 150: 1029-1041

  • DOI: 10.1016/j.cell.2012.06.050
  • Primary Citation of Related Structures:  
    4FMA, 4FMB, 4FMC, 4FMD, 4FME

  • PubMed Abstract: 

    • Rab GTPases are frequent targets of vacuole-living bacterial pathogens for appropriate trafficking of the vacuole. Here we discover that bacterial effectors including VirA from nonvacuole Shigella flexneri and EspG from extracellular Enteropathogenic Esc ...

    Rab GTPases are frequent targets of vacuole-living bacterial pathogens for appropriate trafficking of the vacuole. Here we discover that bacterial effectors including VirA from nonvacuole Shigella flexneri and EspG from extracellular Enteropathogenic Escherichia coli (EPEC) harbor TBC-like dual-finger motifs and exhibits potent RabGAP activities. Specific inactivation of Rab1 by VirA/EspG disrupts ER-to-Golgi trafficking. S. flexneri intracellular persistence requires VirA TBC-like GAP activity that mediates bacterial escape from autophagy-mediated host defense. Rab1 inactivation by EspG severely blocks host secretory pathway, resulting in inhibited interleukin-8 secretion from infected cells. Crystal structures of VirA/EspG-Rab1-GDP-aluminum fluoride complexes highlight TBC-like catalytic role for the arginine and glutamine finger residues and reveal a 3D architecture distinct from that of the TBC domain. Structure of Arf6-EspG-Rab1 ternary complex illustrates a pathogenic signaling complex that rewires host Arf signaling to Rab1 inactivation. Structural distinctions of VirA/EspG further predict a possible extensive presence of TBC-like RabGAP effectors in counteracting various host defenses.

    Organizational Affiliation: 

    National Institute of Biological Sciences, Beijing 102206, China.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
EspG protein A, D351Escherichia coliMutation(s): 0 
Gene Names: espG
Find proteins for Q7DB50 (Escherichia coli O157:H7)
Explore Q7DB50 
Go to UniProtKB:  Q7DB50
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Ras-related protein Rab-1A B, E171Homo sapiensMutation(s): 0 
Gene Names: RAB1, RAB1A
Find proteins for P62820 (Homo sapiens)
Explore P62820 
Go to UniProtKB:  P62820
NIH Common Fund Data Resources
PHAROS:  P62820
GTEx:  ENSG00000138069
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
ADP-ribosylation factor 6 C, F160Homo sapiensMutation(s): 0 
Gene Names: ARF6
Find proteins for P62330 (Homo sapiens)
Explore P62330 
Go to UniProtKB:  P62330
NIH Common Fund Data Resources
PHAROS:  P62330
GTEx:  ENSG00000165527
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.10 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.208 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 137.222α = 90
b = 137.222β = 90
c = 126.503γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
PHASESphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2012-06-16 
  • Released Date: 2012-09-05 
    • Deposition Author(s): Shao, F., Zhu, Y.

Revision History 

  • Version 1.0: 2012-09-05
    Type: Initial release
  • Version 1.1: 2012-10-03
    Changes: Database references