9HIS | pdb_00009his

Extracellular components BamHIJK of the Bacteroides thetaiotaomicron BAM machinery


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.28 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure of a distinct beta-barrel assembly machinery complex in the Bacteroidota.

Silale, A.Madej, M.Mikruta, K.Frey, A.M.Hart, A.J.Basle, A.Scavenius, C.Enghild, J.J.Trost, M.Hirt, R.P.van den Berg, B.

(2025) Nat Microbiol 10: 2845-2859

  • DOI: https://doi.org/10.1038/s41564-025-02132-2
  • Primary Citation of Related Structures:  
    9HIS, 9HIV, 9HJ3, 9HJM

  • PubMed Abstract: 

    The Gram-negative β-barrel assembly machinery (BAM) complex catalyses the folding and membrane insertion of newly synthesized β-barrel outer membrane proteins. The BAM is structurally conserved, but most studies have focused on Gammaproteobacteria. Here, using single-particle cryogenic electron microscopy, quantitative proteomics and functional assays, we show that the BAM complex is distinct within the Bacteroidota. Cryogenic electron microscopy structures of BAM complexes from the human gut symbiont Bacteroides thetaiotaomicron (3.3 Å) and the human oral pathogen Porphyromonas gingivalis (3.2 Å) show similar, seven-component complexes of ~325 kDa. The complexes are mostly extracellular and comprise canonical BamA and BamD; an integral, essential outer membrane protein, BamG, that associates with BamA; and four surface-exposed lipoproteins: BamH-K. Absent from the BAM in Pseudomonadota, BamG-K form a large, extracellular dome that may confer additional functionality to enable the folding and assembly of β-barrel-surface-exposed lipoprotein complexes that are a hallmark of the Bacteroidota. Our findings develop our understanding of fundamental biological processes in an important bacterial phylum.


  • Organizational Affiliation
    • Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DUF6242 domain-containing proteinA [auth H]493Bacteroides thetaiotaomicron VPI-5482Mutation(s): 0 
UniProt
Find proteins for Q8A1D9 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50))
Explore Q8A1D9 
Go to UniProtKB:  Q8A1D9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8A1D9
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomeraseB [auth I]196Bacteroides thetaiotaomicron VPI-5482Mutation(s): 0 
EC: 5.2.1.8
UniProt
Find proteins for Q8A1P7 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50))
Explore Q8A1P7 
Go to UniProtKB:  Q8A1P7
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UniProt GroupQ8A1P7
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DUF4827 domain-containing proteinC [auth J]214Bacteroides thetaiotaomicron VPI-5482Mutation(s): 0 
UniProt
Find proteins for Q8A0S2 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50))
Explore Q8A0S2 
Go to UniProtKB:  Q8A0S2
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UniProt GroupQ8A0S2
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DUF4270 domain-containing proteinD [auth G]525Bacteroides thetaiotaomicron VPI-5482Mutation(s): 0 
UniProt
Find proteins for Q89ZS0 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50))
Explore Q89ZS0 
Go to UniProtKB:  Q89ZS0
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UniProt GroupQ89ZS0
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.28 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom214222/Z/18/Z

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-27
    Type: Initial release
  • Version 1.1: 2025-11-19
    Changes: Data collection, Database references