7NCS

Lateral-open conformation of the lid-locked BAM complex (BamA E435C S665C, BamBDCE) bound by a bactericidal Fab fragment


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The role of membrane destabilisation and protein dynamics in BAM catalysed OMP folding.

White, P.Haysom, S.F.Iadanza, M.G.Higgins, A.J.Machin, J.M.Whitehouse, J.M.Horne, J.E.Schiffrin, B.Carpenter-Platt, C.Calabrese, A.N.Storek, K.M.Rutherford, S.T.Brockwell, D.J.Ranson, N.A.Radford, S.E.

(2021) Nat Commun 12: 4174-4174

  • DOI: https://doi.org/10.1038/s41467-021-24432-x
  • Primary Citation of Related Structures:  
    7BM5, 7BNQ, 7NBX, 7NCS, 7ND0

  • PubMed Abstract: 

    The folding of β-barrel outer membrane proteins (OMPs) in Gram-negative bacteria is catalysed by the β-barrel assembly machinery (BAM). How lateral opening in the β-barrel of the major subunit BamA assists in OMP folding, and the contribution of membrane disruption to BAM catalysis remain unresolved. Here, we use an anti-BamA monoclonal antibody fragment (Fab1) and two disulphide-crosslinked BAM variants (lid-locked (LL), and POTRA-5-locked (P5L)) to dissect these roles. Despite being lethal in vivo, we show that all complexes catalyse folding in vitro, albeit less efficiently than wild-type BAM. CryoEM reveals that while Fab1 and BAM-P5L trap an open-barrel state, BAM-LL contains a mixture of closed and contorted, partially-open structures. Finally, all three complexes globally destabilise the lipid bilayer, while BamA does not, revealing that the BAM lipoproteins are required for this function. Together the results provide insights into the role of BAM structure and lipid dynamics in OMP folding.


  • Organizational Affiliation

    Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Outer membrane protein assembly factor BamA810Escherichia coli K-12Mutation(s): 4 
Gene Names: bamAyaeTyzzNyzzYb0177JW0172
Membrane Entity: Yes 
UniProt
Find proteins for P0A940 (Escherichia coli (strain K12))
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Go to UniProtKB:  P0A940
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UniProt GroupP0A940
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Outer membrane protein assembly factor BamB392Escherichia coli K-12Mutation(s): 0 
Gene Names: bamByfgLb2512JW2496
Membrane Entity: Yes 
UniProt
Find proteins for P77774 (Escherichia coli (strain K12))
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Go to UniProtKB:  P77774
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UniProt GroupP77774
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Outer membrane protein assembly factor BamC344Escherichia coli K-12Mutation(s): 0 
Gene Names: bamCdapXnlpBb2477JW2462
Membrane Entity: Yes 
UniProt
Find proteins for P0A903 (Escherichia coli (strain K12))
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Go to UniProtKB:  P0A903
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UniProt GroupP0A903
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Outer membrane protein assembly factor BamD245Escherichia coli K-12Mutation(s): 0 
Gene Names: bamDyfiOb2595JW2577
Membrane Entity: Yes 
UniProt
Find proteins for P0AC02 (Escherichia coli (strain K12))
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UniProt GroupP0AC02
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Outer membrane protein assembly factor BamE123Escherichia coli K-12Mutation(s): 0 
Gene Names: bamEsmpAb2617JW2598
Membrane Entity: Yes 
UniProt
Find proteins for P0A937 (Escherichia coli (strain K12))
Explore P0A937 
Go to UniProtKB:  P0A937
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UniProt GroupP0A937
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Fab1 heavy chainF [auth H]228Homo sapiensMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Fab1 light chainG [auth L]215Homo sapiensMutation(s): 0 
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0
RECONSTRUCTIONcryoSPARC2.2.0
MODEL REFINEMENTNAMD
MODEL REFINEMENTMDFF
MODEL REFINEMENTVMD
MODEL REFINEMENTPHENIX1.14
MODEL REFINEMENTCoot0.9

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United KingdomMR/P018491/1
Wellcome TrustUnited Kingdom108466/Z/15/Z
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/M011151/1
Wellcome TrustUnited Kingdom222373/Z/21/Z
Wellcome TrustUnited Kingdom105220/Z/14/Z
Research Foundation - Flanders (FWO)BelgiumG0G0818N
Royal SocietyUnited KingdomRSRP/R1/211057

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-02
    Type: Initial release
  • Version 1.1: 2021-07-21
    Changes: Database references