3JQO

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.227 

wwPDB Validation 3D Report Full Report


This is version 1.3 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: 10.1038/nature08588

  • 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 ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TraF protein
A, D, G, J, M, P, S, V, Y, b, e, h, k, n
227Escherichia coliMutation(s): 0 
Gene Names: traF
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Outer Membrane Proteins
Protein: 
Type IV outer membrane secretion complex
Find proteins for Q46705 (Escherichia coli)
Go to UniProtKB:  Q46705
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
TraO protein
B, E, H, K, N, Q, T, W, Z, c, f, i, l, o
135Escherichia coliMutation(s): 0 
Gene Names: traO
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Outer Membrane Proteins
Protein: 
Type IV outer membrane secretion complex
Find proteins for Q46704 (Escherichia coli)
Go to UniProtKB:  Q46704
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
TraN protein
C, F, I, L, O, R, U, X, a, d, g, j, m, p
34Escherichia coliMutation(s): 0 
Gene Names: traN
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Outer Membrane Proteins
Protein: 
Type IV outer membrane secretion complex
Find proteins for Q46702 (Escherichia coli)
Go to UniProtKB:  Q46702
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LDA
Query on LDA

Download SDF File 
Download CCD File 
J
LAURYL DIMETHYLAMINE-N-OXIDE
C14 H31 N O
SYELZBGXAIXKHU-UHFFFAOYSA-N
 Ligand Interaction
MPD
Query on MPD

Download SDF File 
Download CCD File 
D, h, k
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, b, c, D, E, e, f, G, H, h, i, J, K, k, l, M, N, n, o, P, Q, S, T, V, W, Y, Z
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.227 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 202.400α = 90.00
b = 211.630β = 90.00
c = 203.440γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
ADSCdata collection
REFMACrefinement
AMoREphasing
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-12-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2014-02-12
    Type: Database references
  • Version 1.3: 2014-07-23
    Type: Other