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- PDB-9hjm: Porphyromonas gingivalis BAM complex -

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Basic information

Entry
Database: PDB / ID: 9hjm
TitlePorphyromonas gingivalis BAM complex
Components
  • DUF4270 domain-containing protein
  • DUF4827 domain-containing protein
  • DUF6242 domain-containing protein
  • Outer membrane protein
  • Peptidyl-prolyl cis-trans isomerase
  • Putative outer membrane protein
KeywordsMEMBRANE PROTEIN / Outer membrane biogenesis / beta-barrel assembly machinery / BAM / Gram-negative bacteria
Function / homology
Function and homology information


membrane assembly / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / cell outer membrane
Similarity search - Function
Protein of unknown function DUF4827 / Domain of unknown function (DUF4827) / Protein of unknown function DUF4270 / Domain of unknown function (DUF4270) / Outer membrane protein assembly factor BamA / POTRA domain, BamA/TamA-like / Surface antigen variable number repeat / Surface antigen D15-like / POTRA domain / POTRA domain profile. ...Protein of unknown function DUF4827 / Domain of unknown function (DUF4827) / Protein of unknown function DUF4270 / Domain of unknown function (DUF4270) / Outer membrane protein assembly factor BamA / POTRA domain, BamA/TamA-like / Surface antigen variable number repeat / Surface antigen D15-like / POTRA domain / POTRA domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / Peptidyl-prolyl cis-trans isomerase domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
PALMITIC ACID / (2S)-3-hydroxypropane-1,2-diyl dihexadecanoate / Peptidyl-prolyl cis-trans isomerase / Putative outer membrane protein / DUF4827 domain-containing protein / Outer membrane protein / DUF4270 domain-containing protein
Similarity search - Component
Biological speciesPorphyromonas gingivalis ATCC 33277 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.24 Å
AuthorsMadej, M. / Silale, A. / van den Berg, B.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science CentreMO-2023/51/D/NZ1/02675 Poland
CitationJournal: Nat Microbiol / Year: 2025
Title: Structure of a distinct β-barrel assembly machinery complex in the Bacteroidota.
Authors: Augustinas Silale / Mariusz Madej / Katarzyna Mikruta / Andrew M Frey / Adam J Hart / Arnaud Baslé / Carsten Scavenius / Jan J Enghild / Matthias Trost / Robert P Hirt / Bert van den Berg /
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, ...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.
History
DepositionNov 29, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
F: Outer membrane protein
G: DUF4270 domain-containing protein
H: DUF6242 domain-containing protein
I: Peptidyl-prolyl cis-trans isomerase
J: DUF4827 domain-containing protein
A: Putative outer membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)298,6558
Polymers297,8306
Non-polymers8252
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 6 types, 6 molecules FGHIJA

#1: Protein Outer membrane protein / BamG


Mass: 48549.336 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas gingivalis ATCC 33277 (bacteria)
Gene: PGN_1514
Production host: Porphyromonas gingivalis ATCC 33277 (bacteria)
References: UniProt: B2RKY8
#2: Protein DUF4270 domain-containing protein / BamH


Mass: 51849.527 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas gingivalis ATCC 33277 (bacteria)
Gene: PGN_1735
Production host: Porphyromonas gingivalis ATCC 33277 (bacteria)
References: UniProt: B2RLK9
#3: Protein DUF6242 domain-containing protein / BamI


Mass: 50949.676 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas gingivalis ATCC 33277 (bacteria)
Production host: Porphyromonas gingivalis ATCC 33277 (bacteria)
#4: Protein Peptidyl-prolyl cis-trans isomerase / BamJ


Mass: 20946.074 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas gingivalis ATCC 33277 (bacteria)
Gene: PGN_0208
Production host: Porphyromonas gingivalis ATCC 33277 (bacteria)
References: UniProt: B2RH82, peptidylprolyl isomerase
#5: Protein DUF4827 domain-containing protein / BamK


Mass: 23531.420 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas gingivalis ATCC 33277 (bacteria)
Gene: PGN_1188
Production host: Porphyromonas gingivalis ATCC 33277 (bacteria)
References: UniProt: B2RK12
#6: Protein Putative outer membrane protein / BamA


Mass: 102003.773 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas gingivalis ATCC 33277 (bacteria)
Gene: PGN_0299
Production host: Porphyromonas gingivalis ATCC 33277 (bacteria)
References: UniProt: B2RHH3

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Non-polymers , 2 types, 2 molecules

#7: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2
#8: Chemical ChemComp-Z41 / (2S)-3-hydroxypropane-1,2-diyl dihexadecanoate


Mass: 568.911 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H68O5

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Porphyromonas gingivalis BAM complex / Type: COMPLEX / Entity ID: #1-#6 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Porphyromonas gingivalis ATCC 33277 (bacteria)
Source (recombinant)Organism: Porphyromonas gingivalis ATCC 33277 (bacteria)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
1100 mMsodium chlorideNaCl1
210 mMHEPESHEPES1
30.03 %dodecyl maltosideDDM1
SpecimenConc.: 4.9 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 1500 nm / Nominal defocus min: 600 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 41.01 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of real images: 11459
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategoryDetails
2EPU2.10.0.1941RELimage acquisition
7PHENIXmodel fittingdock in map
9PHENIX1.21.1_5286:model refinementreal space refine
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.24 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 86584 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model building
ID 3D fitting-IDChain-IDSource nameType
11AAlphaFoldin silico model
21FAlphaFoldin silico model
31GAlphaFoldin silico model
41HAlphaFoldin silico model
51IAlphaFoldin silico model
61JAlphaFoldin silico model

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