9HJM | pdb_00009hjm

Porphyromonas gingivalis BAM complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.24 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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


This is version 1.0 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
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Outer membrane proteinA [auth F]434Porphyromonas gingivalis ATCC 33277Mutation(s): 0 
Gene Names: PGN_1514
UniProt
Find proteins for B2RKY8 (Porphyromonas gingivalis (strain ATCC 33277 / DSM 20709 / CIP 103683 / JCM 12257 / NCTC 11834 / 2561))
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Go to UniProtKB:  B2RKY8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB2RKY8
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DUF4270 domain-containing proteinB [auth G]462Porphyromonas gingivalis ATCC 33277Mutation(s): 0 
Gene Names: PGN_1735
UniProt
Find proteins for B2RLK9 (Porphyromonas gingivalis (strain ATCC 33277 / DSM 20709 / CIP 103683 / JCM 12257 / NCTC 11834 / 2561))
Explore B2RLK9 
Go to UniProtKB:  B2RLK9
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UniProt GroupB2RLK9
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DUF6242 domain-containing proteinC [auth H]456Porphyromonas gingivalis ATCC 33277Mutation(s): 0 
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomeraseD [auth I]185Porphyromonas gingivalis ATCC 33277Mutation(s): 0 
Gene Names: PGN_0208
EC: 5.2.1.8
UniProt
Find proteins for B2RH82 (Porphyromonas gingivalis (strain ATCC 33277 / DSM 20709 / CIP 103683 / JCM 12257 / NCTC 11834 / 2561))
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Go to UniProtKB:  B2RH82
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UniProt GroupB2RH82
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
DUF4827 domain-containing proteinE [auth J]203Porphyromonas gingivalis ATCC 33277Mutation(s): 0 
Gene Names: PGN_1188
UniProt
Find proteins for B2RK12 (Porphyromonas gingivalis (strain ATCC 33277 / DSM 20709 / CIP 103683 / JCM 12257 / NCTC 11834 / 2561))
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Go to UniProtKB:  B2RK12
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UniProt GroupB2RK12
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Putative outer membrane proteinF [auth A]891Porphyromonas gingivalis ATCC 33277Mutation(s): 0 
Gene Names: PGN_0299
UniProt
Find proteins for B2RHH3 (Porphyromonas gingivalis (strain ATCC 33277 / DSM 20709 / CIP 103683 / JCM 12257 / NCTC 11834 / 2561))
Explore B2RHH3 
Go to UniProtKB:  B2RHH3
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UniProt GroupB2RHH3
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Z41
Query on Z41

Download Ideal Coordinates CCD File 
H [auth G](2S)-3-hydroxypropane-1,2-diyl dihexadecanoate
C35 H68 O5
JEJLGIQLPYYGEE-XIFFEERXSA-N
PLM
Query on PLM

Download Ideal Coordinates CCD File 
G
PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.24 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.1_5286:
RECONSTRUCTIONcryoSPARC

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Polish National Science CentrePolandMO-2023/51/D/NZ1/02675

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-19
    Type: Initial release