3JQO

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

PDB DOI: https://doi.org/10.2210/pdb3JQO/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli
Mutation(s): No
Membrane Protein: Yes OPMPDBTMmpstruc

Deposited: 2009-09-07 Released: 2009-12-01
Deposition Author(s): Chandran, V., Fronzes, R., Duquerroy, S., Cronin, N., Navaza, J., Waksman, G.

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

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 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

PubMed: 19946264 Search on PubMedSearch on PubMed Central
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.

Macromolecule Content

Total Structure Weight: 606.12 kDa
Atom Count: 38,842
Modelled Residue Count: 4,909
Deposited Residue Count: 5,544
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TraF protein	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	227	Escherichia coli K-12	Mutation(s): 0 Gene Names: traF Membrane Entity: Yes
UniProt
Find proteins for Q46705 (Escherichia coli) Explore Q46705 Go to UniProtKB: Q46705
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q46705
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
TraO protein	B CA [auth c] E FA [auth f] H B, CA [auth c], E, FA [auth f], H, IA [auth i], K, LA [auth l], N, OA [auth o], Q, T, W, Z	135	Escherichia coli K-12	Mutation(s): 0 Gene Names: traO Membrane Entity: Yes
UniProt
Find proteins for Q46704 (Escherichia coli) Explore Q46704 Go to UniProtKB: Q46704
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q46704
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
TraN protein	AA [auth a] C DA [auth d] F GA [auth g] AA [auth a], C, DA [auth d], F, GA [auth g], I, JA [auth j], L, MA [auth m], O, PA [auth p], R, U, X	34	Escherichia coli K-12	Mutation(s): 0 Gene Names: traN
UniProt
Find proteins for Q46702 (Escherichia coli) Explore Q46702 Go to UniProtKB: Q46702
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q46702
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LDA Query on LDA Download Ideal Coordinates CCD File SDF format, chain RA [auth J] MOL2 format, chain RA [auth J]	RA [auth J]	LAURYL DIMETHYLAMINE-N-OXIDE C₁₄ H₃₁ N O SYELZBGXAIXKHU-UHFFFAOYSA-N		Interactions Focus chain RA [auth J] Interactions & Density Focus chain RA [auth J]
MPD Query on MPD Download Ideal Coordinates CCD File SDF format, chain QA [auth D] SDF format, chain SA [auth h] SDF format, chain TA [auth k] MOL2 format, chain QA [auth D] MOL2 format, chain SA [auth h] MOL2 format, chain TA [auth k]	QA [auth D], SA [auth h], TA [auth k]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain QA [auth D] Focus chain SA [auth h] Focus chain TA [auth k] Interactions & Density Focus chain QA [auth D] Focus chain SA [auth h] Focus chain TA [auth k]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
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 LINKING	C₅ H₁₁ N O₂ Se		MET

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 = 202.4	α = 90
b = 211.63	β = 90
c = 203.44	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
AMoRE	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2009-12-01

Deposition Author(s):

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
Version 1.5: 2024-04-03
Changes: Data collection, Database references, Derived calculations, Refinement description