3JQO

Crystal structure of the outer membrane complex of a type IV secretion system


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.229 

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This is version 1.4 of the entry. See complete history


Literature

Structure of the outer membrane complex of a type IV secretion system

Chandran, V.Fronzes, R.Duquerroy, S.Cronin, N.Navaza, J.Waksman, G.

(2009) Nature 462: 1011-1015

  • DOI: https://doi.org/10.1038/nature08588
  • Primary Citation of Related Structures:  
    3JQO

  • PubMed Abstract: 

    Type IV secretion systems are secretion nanomachines spanning the two membranes of Gram-negative bacteria. Three proteins, VirB7, VirB9 and VirB10, assemble into a 1.05 megadalton (MDa) core spanning the inner and outer membranes. This core consists of 14 copies of each of the proteins and forms two layers, the I and O layers, inserting in the inner and outer membrane, respectively. Here we present the crystal structure of a approximately 0.6 MDa outer-membrane complex containing the entire O layer. This structure is the largest determined for an outer-membrane channel and is unprecedented in being composed of three proteins. Unexpectedly, this structure identifies VirB10 as the outer-membrane channel with a unique hydrophobic double-helical transmembrane region. This structure establishes VirB10 as the only known protein crossing both membranes of Gram-negative bacteria. Comparison of the cryo-electron microscopy (cryo-EM) and crystallographic structures points to conformational changes regulating channel opening and closing.


  • Organizational Affiliation

    Institute of Structural and Molecular Biology, University College London and Birkbeck College, Malet Street, London WC1E 7HX, UK.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TraF protein227Escherichia coli K-12Mutation(s): 0 
Gene Names: traF
Membrane Entity: Yes 
UniProt
Find proteins for Q46705 (Escherichia coli)
Explore Q46705 
Go to UniProtKB:  Q46705
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ46705
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
TraO protein135Escherichia coli K-12Mutation(s): 0 
Gene Names: traO
Membrane Entity: Yes 
UniProt
Find proteins for Q46704 (Escherichia coli)
Explore Q46704 
Go to UniProtKB:  Q46704
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ46704
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
TraN protein34Escherichia coli K-12Mutation(s): 0 
Gene Names: traN
UniProt
Find proteins for Q46702 (Escherichia coli)
Explore Q46702 
Go to UniProtKB:  Q46702
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ46702
Sequence Annotations
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
BA [auth b]
D
EA [auth e]
G
A,
BA [auth b],
D,
EA [auth e],
G,
HA [auth h],
J,
KA [auth k],
M,
NA [auth n],
P,
S,
V,
Y
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.229 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 202.4α = 90
b = 211.63β = 90
c = 203.44γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
AMoREphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-12-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2014-02-12
    Changes: Database references
  • Version 1.3: 2014-07-23
    Changes: Other
  • Version 1.4: 2019-11-20
    Changes: Database references, Derived calculations