6T1W | pdb_00006t1w

Structure of E. coli BamA in complex with lipoprotein RcsF


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.79 Å
  • R-Value Free: 
    0.317 (Depositor), 0.359 (DCC) 
  • R-Value Work: 
    0.281 (Depositor), 0.313 (DCC) 
  • R-Value Observed: 
    0.283 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6T1W

This is version 1.4 of the entry. See complete history

Literature

Structural insight into the formation of lipoprotein-beta-barrel complexes.

Rodriguez-Alonso, R.Letoquart, J.Nguyen, V.S.Louis, G.Calabrese, A.N.Iorga, B.I.Radford, S.E.Cho, S.H.Remaut, H.Collet, J.F.

(2020) Nat Chem Biol 16: 1019-1025

  • DOI: https://doi.org/10.1038/s41589-020-0575-0
  • Primary Citation Related Structures: 
    6T1W

  • PubMed Abstract: 

    The β-barrel assembly machinery (BAM) inserts outer membrane β-barrel proteins (OMPs) in the outer membrane of Gram-negative bacteria. In Enterobacteriacea, BAM also mediates export of the stress sensor lipoprotein RcsF to the cell surface by assembling RcsF-OMP complexes. Here, we report the crystal structure of the key BAM component BamA in complex with RcsF. BamA adopts an inward-open conformation, with the lateral gate to the membrane closed. RcsF is lodged deep within the lumen of the BamA barrel, binding regions proposed to undergo outward and lateral opening during OMP insertion. On the basis of our structural and biochemical data, we propose a push-and-pull model for RcsF export following conformational cycling of BamA, and provide a mechanistic explanation for how RcsF uses its interaction with BamA to detect envelope stress. Our data also suggest that the flux of incoming OMP substrates is involved in the control of BAM activity.


  • Organizational Affiliation
    • Walloon Excellence in Life Sciences and Biotechnology, Brussels, Belgium.

Macromolecule Content 

  • Total Structure Weight: 209.65 kDa 
  • Atom Count: 10,838 
  • Modeled Residue Count: 1,388 
  • Deposited Residue Count: 1,888 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Outer membrane protein assembly factor BamA
A, B
810Escherichia coli K-12Mutation(s): 0 
Gene Names: bamAyaeTyzzNyzzYb0177JW0172
Membrane Entity: Yes 
UniProt
Find proteins for P0A940 (Escherichia coli (strain K12))
Explore P0A940 
Go to UniProtKB:  P0A940
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A940
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Outer membrane lipoprotein RcsF
C, D
134Escherichia coli K-12Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P69411 (Escherichia coli (strain K12))
Explore P69411 
Go to UniProtKB:  P69411
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP69411
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.79 Å
  • R-Value Free:  0.317 (Depositor), 0.359 (DCC) 
  • R-Value Work:  0.281 (Depositor), 0.313 (DCC) 
  • R-Value Observed: 0.283 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 158.84α = 90
b = 142.53β = 102.61
c = 116.42γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
STARANISOdata scaling

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Research Foundation - FlandersBelgium--
Walloon Excellence in Lifesciences & BIOtechnologyBelgium--

Revision History  (Full details and data files)

  • Version 1.0: 2020-05-13
    Type: Initial release
  • Version 1.1: 2020-07-22
    Changes: Database references
  • Version 1.2: 2020-08-26
    Changes: Database references
  • Version 1.3: 2024-01-24
    Changes: Data collection, Database references, Refinement description
  • Version 1.4: 2024-11-13
    Changes: Structure summary