4KSR | pdb_00004ksr

Crystal Structure of the Vibrio cholerae ATPase GspE Hexamer

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.20 Å
  • R-Value Free: 
    0.376 (Depositor), 0.384 (DCC) 
  • R-Value Work: 
    0.384 (Depositor), 0.389 (DCC) 
  • R-Value Observed: 
    0.384 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history. 

Literature

Hexamers of the Type II Secretion ATPase GspE from Vibrio cholerae with Increased ATPase Activity.

Lu, C., Turley, S., Marionni, S.T., Park, Y.J., Lee, K.K., Patrick, M., Shah, R., Sandkvist, M., Bush, M.F., Hol, W.G.

(2013) Structure 21: 1707-1717

  • DOI: https://doi.org/10.1016/j.str.2013.06.027
  • Primary Citation Related Structures: 
    4KSR, 4KSS

  • PubMed Abstract: 

    The type II secretion system (T2SS), a multiprotein machinery spanning two membranes in Gram-negative bacteria, is responsible for the secretion of folded proteins from the periplasm across the outer membrane. The critical multidomain T2SS assembly ATPase GspE(EpsE) had not been structurally characterized as a hexamer. Here, four hexamers of Vibrio cholerae GspE(EpsE) are obtained when fused to Hcp1 as an assistant hexamer, as shown with native mass spectrometry. The enzymatic activity of the GspE(EpsE)-Hcp1 fusions is ∼20 times higher than that of a GspE(EpsE) monomer, indicating that increasing the local concentration of GspE(EpsE) by the fusion strategy was successful. Crystal structures of GspE(EpsE)-Hcp1 fusions with different linker lengths reveal regular and elongated hexamers of GspE(EpsE) with major differences in domain orientation within subunits, and in subunit assembly. SAXS studies on GspE(EpsE)-Hcp1 fusions suggest that even further variability in GspE(EpsE) hexamer architecture is likely.

    • Organizational Affiliation: 
    • Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.

Macromolecule Content 

  • Total Structure Weight: 192.88 kDa 
  • Atom Count: 12,063 
  • Modeled Residue Count: 1,563 
  • Deposited Residue Count: 1,749 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Type II secretion system protein E, Hemolysin-coregulated protein
A, B, C
583Vibrio cholerae O1 biovar El Tor str. N16961, Pseudomonas aeruginosa UCBPP-PA14
This entity is chimeric		Mutation(s): 0 
Gene Names: epsE, VC_2732, PA14_01030
EC: 7.4.2.8
UniProt
Find proteins for A0A0H2ZJ24 (Pseudomonas aeruginosa (strain UCBPP-PA14))
Explore A0A0H2ZJ24 
Go to UniProtKB:  A0A0H2ZJ24
Find proteins for P37093 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961))
Explore P37093 
Go to UniProtKB:  P37093
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP37093A0A0H2ZJ24
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.20 Å
  • R-Value Free:  0.376 (Depositor), 0.384 (DCC) 
  • R-Value Work:  0.384 (Depositor), 0.389 (DCC) 
  • R-Value Observed: 0.384 (Depositor) 
Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.467α = 90
b = 132.911β = 90
c = 142.75γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata scaling
PHASESphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-09-04
    Type: Initial release
  • Version 1.1: 2013-10-09
    Changes: Database references
  • Version 1.2: 2017-08-23
    Changes: Refinement description, Source and taxonomy
  • Version 1.3: 2024-02-28
    Changes: Data collection, Database references