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- EMDB-52202: BamADG components of the Bacteroides thetaiotaomicron BAM machinery -

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Basic information

Entry
Database: EMDB / ID: EMD-52202
TitleBamADG components of the Bacteroides thetaiotaomicron BAM machinery
Map dataunsharpened map
Sample
  • Complex: BamADF components of the Bacteroides thetaiotaomicron BAM complex
    • Protein or peptide: Outer membrane protein
    • Protein or peptide: Lipoprotein protein, putative
    • Protein or peptide: Outer membrane protein
KeywordsOuter membrane protein biogenesis / Beta-barrel assembly machinery / BAM / MEMBRANE PROTEIN
Function / homology
Function and homology information


membrane assembly / cell outer membrane
Similarity search - Function
Outer membrane protein transport protein (OMPP1/FadL/TodX) / Outer membrane protein transport protein (OMPP1/FadL/TodX) / Outer membrane protein assembly factor BamD / Outer membrane lipoprotein BamD-like / Outer membrane lipoprotein / Outer membrane protein assembly factor BamA / POTRA domain, BamA/TamA-like / Surface antigen variable number repeat / Surface antigen D15-like / POTRA domain ...Outer membrane protein transport protein (OMPP1/FadL/TodX) / Outer membrane protein transport protein (OMPP1/FadL/TodX) / Outer membrane protein assembly factor BamD / Outer membrane lipoprotein BamD-like / Outer membrane lipoprotein / 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. / Bacterial surface antigen (D15) / Omp85 superfamily domain / TPR repeat profile. / Tetratricopeptide repeat / Prokaryotic membrane lipoprotein lipid attachment site profile. / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
Outer membrane protein / Outer membrane protein / Lipoprotein protein, putative
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron VPI-5482 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.46 Å
AuthorsSilale A / van den Berg B
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Wellcome Trust214222/Z/18/Z United Kingdom
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 27, 2024-
Header (metadata) releaseAug 27, 2025-
Map releaseAug 27, 2025-
UpdateNov 19, 2025-
Current statusNov 19, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52202.png

Downloads & links

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Map

FileDownload / File: emd_52202.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationunsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.74 Å/pix.
x 448 pix.
= 331.52 Å		0.74 Å/pix.
x 448 pix.
= 331.52 Å		0.74 Å/pix.
x 448 pix.
= 331.52 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.74 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0645
Minimum - Maximum-0.2014325 - 0.36448744
Average (Standard dev.)0.0011941806 (±0.00976889)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 331.52002 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_52202_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

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Additional map: sharpened map

Fileemd_52202_additional_1.map
Annotationsharpened map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_52202_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_52202_half_map_2.map
Annotationhalf map B
Projections & Slices
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Sample components

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Entire : BamADF components of the Bacteroides thetaiotaomicron BAM complex

EntireName: BamADF components of the Bacteroides thetaiotaomicron BAM complex
Components
  • Complex: BamADF components of the Bacteroides thetaiotaomicron BAM complex
    • Protein or peptide: Outer membrane protein
    • Protein or peptide: Lipoprotein protein, putative
    • Protein or peptide: Outer membrane protein

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Supramolecule #1: BamADF components of the Bacteroides thetaiotaomicron BAM complex

SupramoleculeName: BamADF components of the Bacteroides thetaiotaomicron BAM complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Molecular weightTheoretical: 173 KDa

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Macromolecule #1: Outer membrane protein

MacromoleculeName: Outer membrane protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Molecular weightTheoretical: 102.494711 KDa
Recombinant expressionOrganism: Bacteroides thetaiotaomicron VPI-5482 (bacteria)
SequenceString: MHYRISFIFV TFICLFCFAA TGFTQNTNHH HHHHHTDEDS KPVILYSGTP KKYEIADIKV EGVKNYEDYV LIGLSGLSVG QTITVPGDE ITGAIKRYWK HGLFSNVQIT AEKIEGNKIW LKISLTQRPR IADVRYHGVK KSERTDFESK LGMVKGMQIT P NTVDRAKT ...String:
MHYRISFIFV TFICLFCFAA TGFTQNTNHH HHHHHTDEDS KPVILYSGTP KKYEIADIKV EGVKNYEDYV LIGLSGLSVG QTITVPGDE ITGAIKRYWK HGLFSNVQIT AEKIEGNKIW LKISLTQRPR IADVRYHGVK KSERTDFESK LGMVKGMQIT P NTVDRAKT LIKRYFDDKG FKNAEVIIAQ KDDPSNENQV IVDIDIDKKE KIKVHAIHIT GNSAIKTSKL KKVMKKTNEK GK LLNLFRT KKFVPENFEA DKQLIIDKYN ELGYRDAMIV KDSVAQYDEK TVDVYMDIDE GQKYYLRNVT WVGNTLYPSE QLN FLLRMK KGDVYNQKLL GERTSTDDDA IGNLYYNNGY LFYNLDPVEV NIVGDSIDLE MRIYEGRQAT INKINISGND RLYE NVVRR ELRIRPGQLF SKDDLMRSLR EIQQMGHFDP EKLQPDIQPD PVNGTVDIGL PLTSKANDQV EFSAGWGQTG IIGKL SLKF TNFSVANLLR PGENYRGILP QGDGQTLTIS GQTNAKYYQS YSISFFDPWF GGKRPNSLSV SAFFSVQTDI SSRYYN SSY FNNYYNSMYS GYGGYGMYNY GNYNNYENYY DPDKSIKMWG LSLGWGKRLK WPDDYFTLSA ELAYQRYNLK DWQYFPV TN GKCNDLSLSL TLARNSIDNP IFPRTGSDFS LSVQLTPPYS LFDGKDYKGY FYDPTDDRGI TQDNMNKLHR WVEYHKWK F KAKTYTPLMD YIAHPKCLVL MTRTEFGLLG HYNKYKKSPF GTFDVGGDGM TGYSSYATES IALRGYENSS LTPYGKEGY AYARLGIELR YPLMLETSTN IYVLGFLEAG NAWHDISKFN PFDLKRSAGI GVRIFLPMIG MMGIDWGYGF DKINGSKEYG GSQFHFILG QEF

UniProtKB: Outer membrane protein

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Macromolecule #2: Lipoprotein protein, putative

MacromoleculeName: Lipoprotein protein, putative / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Molecular weightTheoretical: 31.415555 KDa
SequenceString: MKKNIIITLL AAASLTSCGE YNKLLKSTDY EYKYEAAKNY FAKGQYNRSA TLLNELITIL KGTDKAEESL YMLGMSYYNQ KDYQTAAQT FITYFNTYPR GTFTELARFH AGKSLFLDTP EPRLDQSSTY QAIQQLQMFM EYFPNSTKKQ EAQDMIFALQ D KLVLKELY ...String:
MKKNIIITLL AAASLTSCGE YNKLLKSTDY EYKYEAAKNY FAKGQYNRSA TLLNELITIL KGTDKAEESL YMLGMSYYNQ KDYQTAAQT FITYFNTYPR GTFTELARFH AGKSLFLDTP EPRLDQSSTY QAIQQLQMFM EYFPNSTKKQ EAQDMIFALQ D KLVLKELY SAKLYYNLGN YLGNNYESCV ITAQNALKDY PYTDYREELS ILILRARHEM AIYSVEDKKM DRYRETIDEY YA FKNEFPE SKYLKEAEKI FNESQKVIKD

UniProtKB: Lipoprotein protein, putative

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Macromolecule #3: Outer membrane protein

MacromoleculeName: Outer membrane protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Molecular weightTheoretical: 47.860691 KDa
SequenceString: MVGFKHTIWA LLLMMVTGTA IAQNNTNSPY TRYGYGDLSD QSFGNSKAMG GIAFGLRDGA QINPTNPASY TAIDSLTFLF EGGVSLQNM NISGGGLKLN AKNASFDYLA MQFRLAPWMA MSVGLLPYSN VGYTVSDSQT TDNGLAYSRS FTGDGGLHQM Y VGAGVKVL ...String:
MVGFKHTIWA LLLMMVTGTA IAQNNTNSPY TRYGYGDLSD QSFGNSKAMG GIAFGLRDGA QINPTNPASY TAIDSLTFLF EGGVSLQNM NISGGGLKLN AKNASFDYLA MQFRLAPWMA MSVGLLPYSN VGYTVSDSQT TDNGLAYSRS FTGDGGLHQM Y VGAGVKVL KNLSVGVNAS YFWGDITRTR GMFYPGTSSY DSYQRKMVTS ISDYKLDFGA QYTQALNKKS SLTIGAVYSP KH KLNNDYT SIVIMGASSS SYGTEYKDVL DATFELPNTF GVGFTYNYDK RLTVGADYSL QQWSKTNFGV VTSDENVRQD FNE TFTYCD RTKISVGAEY IPNLIGRSYF AHIKYRLGAY YTTPYYKIDG KKASREYGVT AGFGLPVPRS RSILSISGQF VRVK GLETN MVNENIFRVS IGLTFNERWF FKRRVE

UniProtKB: Outer membrane protein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration8 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
150.0 mMNaClsodium chloride
10.0 mMHEPESHEPES
0.04 %DDMdodecyl maltoside
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 13558 / Average electron dose: 35.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 165000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2266553
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Ab initio reconstruction
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.46 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 56321
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC / Details: Non-uniform refinement
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

1-f1

chain_id: A, source_name: AlphaFold, initial_model_type: in silico model

2-f1

chain_id: D, source_name: AlphaFold, initial_model_type: in silico model

0-f1

chain_id: F, source_name: AlphaFold, initial_model_type: in silico model
DetailsAlphaFold2 models were docked using Phenix.
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 64.9
Output model

PDB-9hiv:
BamADG components of the Bacteroides thetaiotaomicron BAM machinery

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