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- EMDB-52209: Bacteroides thetaiotaomicron BAM complex -

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Basic information

Entry
Database: EMDB / ID: EMD-52209
TitleBacteroides thetaiotaomicron BAM complex
Map dataComposite map
Sample
  • Complex: Bacteroides thetaiotaomicron BAM complex
    • Protein or peptide: Outer membrane protein
    • Protein or peptide: Lipoprotein protein, putative
    • Protein or peptide: Outer membrane protein
    • Protein or peptide: DUF6242 domain-containing protein
    • Protein or peptide: Peptidyl-prolyl cis-trans isomerase
    • Protein or peptide: DUF4827 domain-containing protein
    • Protein or peptide: DUF4270 domain-containing protein
  • Ligand: N-TRIDECANOIC ACID
  • Ligand: (2S)-3-hydroxypropane-1,2-diyl dihexadecanoate
KeywordsOuter membrane protein biogenesis / Beta-barrel assembly machinery / BAM / MEMBRANE PROTEIN
Function / homology
Function and homology information


membrane assembly / peptidylprolyl isomerase / cell outer membrane / peptidyl-prolyl cis-trans isomerase activity
Similarity search - Function
Domain of unknown function DUF6242 / Domain of unknown function (DUF6242) N-terminal domain / Protein of unknown function DUF4827 / Domain of unknown function (DUF4827) / Protein of unknown function DUF4270 / Domain of unknown function (DUF4270) / 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 ...Domain of unknown function DUF6242 / Domain of unknown function (DUF6242) N-terminal domain / Protein of unknown function DUF4827 / Domain of unknown function (DUF4827) / Protein of unknown function DUF4270 / Domain of unknown function (DUF4270) / 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 / 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 / TPR repeat profile. / Tetratricopeptide repeat / Prokaryotic membrane lipoprotein lipid attachment site profile. / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
Outer membrane protein / DUF4270 domain-containing protein / DUF4827 domain-containing protein / DUF6242 domain-containing protein / Outer membrane protein / Peptidyl-prolyl cis-trans isomerase / 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_52209.png

Downloads & links

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Map

FileDownload / File: emd_52209.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (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)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.74 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 5.93
Minimum - Maximum-30.859718000000001 - 45.319980000000001
Average (Standard dev.)0.00296828 (±1.0508018)
SymmetrySpace group: 1
Details

EMDB XML:

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

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Supplemental data

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Sample components

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Entire : Bacteroides thetaiotaomicron BAM complex

EntireName: Bacteroides thetaiotaomicron BAM complex
Components
  • Complex: Bacteroides thetaiotaomicron BAM complex
    • Protein or peptide: Outer membrane protein
    • Protein or peptide: Lipoprotein protein, putative
    • Protein or peptide: Outer membrane protein
    • Protein or peptide: DUF6242 domain-containing protein
    • Protein or peptide: Peptidyl-prolyl cis-trans isomerase
    • Protein or peptide: DUF4827 domain-containing protein
    • Protein or peptide: DUF4270 domain-containing protein
  • Ligand: N-TRIDECANOIC ACID
  • Ligand: (2S)-3-hydroxypropane-1,2-diyl dihexadecanoate

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Supramolecule #1: Bacteroides thetaiotaomicron BAM complex

SupramoleculeName: Bacteroides thetaiotaomicron BAM complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Molecular weightTheoretical: 325 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: 101.527664 KDa
Recombinant expressionOrganism: Bacteroides thetaiotaomicron VPI-5482 (bacteria)
SequenceString: MHYRISFIFV TFICLFCFAA TGFTQNTNTD EDSKPVILYS GTPKKYEIAD IKVEGVKNYE DYVLIGLSGL SVGQTITVPG DEITGAIKR YWKHGLFSNV QITAEKIEGN KIWLKISLTQ RPRIADVRYH GVKKSERTDF ESKLGMVKGM QITPNTVDRA K TLIKRYFD ...String:
MHYRISFIFV TFICLFCFAA TGFTQNTNTD EDSKPVILYS GTPKKYEIAD IKVEGVKNYE DYVLIGLSGL SVGQTITVPG DEITGAIKR YWKHGLFSNV QITAEKIEGN KIWLKISLTQ RPRIADVRYH GVKKSERTDF ESKLGMVKGM QITPNTVDRA K TLIKRYFD DKGFKNAEVI IAQKDDPSNE NQVIVDIDID KKEKIKVHAI HITGNSAIKT SKLKKVMKKT NEKGKLLNLF RT KKFVPEN FEADKQLIID KYNELGYRDA MIVKDSVAQY DEKTVDVYMD IDEGQKYYLR NVTWVGNTLY PSEQLNFLLR MKK GDVYNQ KLLGERTSTD DDAIGNLYYN NGYLFYNLDP VEVNIVGDSI DLEMRIYEGR QATINKINIS GNDRLYENVV RREL RIRPG QLFSKDDLMR SLREIQQMGH FDPEKLQPDI QPDPVNGTVD IGLPLTSKAN DQVEFSAGWG QTGIIGKLSL KFTNF SVAN LLRPGENYRG ILPQGDGQTL TISGQTNAKY YQSYSISFFD PWFGGKRPNS LSVSAFFSVQ TDISSRYYNS SYFNNY YNS MYSGYGGYGM YNYGNYNNYE NYYDPDKSIK MWGLSLGWGK RLKWPDDYFT LSAELAYQRY NLKDWQYFPV TNGKCND LS LSLTLARNSI DNPIFPRTGS DFSLSVQLTP PYSLFDGKDY KGYFYDPTDD RGITQDNMNK LHRWVEYHKW KFKAKTYT P LMDYIAHPKC LVLMTRTEFG LLGHYNKYKK SPFGTFDVGG DGMTGYSSYA TESIALRGYE NSSLTPYGKE GYAYARLGI ELRYPLMLET STNIYVLGFL EAGNAWHDIS KFNPFDLKRS AGIGVRIFLP MIGMMGIDWG YGFDKINGSK EYGGSQFHFI LGQEF

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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Macromolecule #4: DUF6242 domain-containing protein

MacromoleculeName: DUF6242 domain-containing protein / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Molecular weightTheoretical: 55.108051 KDa
SequenceString: MRIKFLSIIA SFFMVSFVIT SCLDNDNEVN YSPDATIRAF ELDTIGYGVN YKFTIDQVSR LIYNVDSLPV NADTIINSIL IKTLTTASG IVTMKDQNDQ DSIVNINDSI DLTKYVNATE KNNFLVLKVW APNMEVQNEY KVNIRMHTMV PDSLSWGKDP I ANNPVRNT ...String:
MRIKFLSIIA SFFMVSFVIT SCLDNDNEVN YSPDATIRAF ELDTIGYGVN YKFTIDQVSR LIYNVDSLPV NADTIINSIL IKTLTTASG IVTMKDQNDQ DSIVNINDSI DLTKYVNATE KNNFLVLKVW APNMEVQNEY KVNIRMHTMV PDSLSWGKDP I ANNPVRNT AEKQKVVTLG DKILLFAQNN EIYSTAIPAG SPTDRLNYGQ KWDKETTGKL PDGADVTSII RFVDKLYLLT KN KEVYNSN DGLTWTKDEV LNSDGVSVTN LITSFSDSDG SNHKKINGIA GIVEINGEKY FSFAEKDVTW EKDIDKLTVV PAE FPINNL SADVYATESG TLNAIVVGNT EDGLDNDTAT VVWASEDGKA WIPMEIPSNN NCPKLVDPSI IHYNDAFYIC GKET KDDAK GFQKFYTSPT LLVWKGVDRM FMLPGILPPV KLEGGVTQHP SLHESSFKGK EVNYTMVVDR NHYIWMVGGQ GIDKI WRGR VNKLGFLIQ

UniProtKB: DUF6242 domain-containing protein

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Macromolecule #5: Peptidyl-prolyl cis-trans isomerase

MacromoleculeName: Peptidyl-prolyl cis-trans isomerase / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO / EC number: peptidylprolyl isomerase
Source (natural)Organism: Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Molecular weightTheoretical: 21.884557 KDa
SequenceString: MSKKIYLFSL VLLALAFVSC SETEEVGKYD NWRARNEAFI DSLANVYATA SGRGGLERIE MLTAPGNYIY YKEMEPMTDH VVKAGNPKY TDYVKVYYKG TNILGEYFDG NFKGDNPVVD GKDPSEGDSP TTIFQVSGVI TGWGEVLQRM EVGDRWKVYI P WDYAYGSS ...String:
MSKKIYLFSL VLLALAFVSC SETEEVGKYD NWRARNEAFI DSLANVYATA SGRGGLERIE MLTAPGNYIY YKEMEPMTDH VVKAGNPKY TDYVKVYYKG TNILGEYFDG NFKGDNPVVD GKDPSEGDSP TTIFQVSGVI TGWGEVLQRM EVGDRWKVYI P WDYAYGSS GTTGILGYSA LVFDITLLDF ANTEAELK

UniProtKB: Peptidyl-prolyl cis-trans isomerase

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Macromolecule #6: DUF4827 domain-containing protein

MacromoleculeName: DUF4827 domain-containing protein / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Molecular weightTheoretical: 24.712709 KDa
SequenceString: MKKLVFLFLS LLAAGGIFQA CDDSKTYAEM LEDEKNAVNK FIKDKGIRII SQDEFEKNDT VTNLERNEYV ALSDGVYMQI VDRGSAENK TDTFANNNEI CVRYIEEDIM TRDTTCFNVF LEEWGDANQL YTNPAVFRYV AEGSYVYGTF IQMDYYWASY Y QSTAVPAG ...String:
MKKLVFLFLS LLAAGGIFQA CDDSKTYAEM LEDEKNAVNK FIKDKGIRII SQDEFEKNDT VTNLERNEYV ALSDGVYMQI VDRGSAENK TDTFANNNEI CVRYIEEDIM TRDTTCFNVF LEEWGDANQL YTNPAVFRYV AEGSYVYGTF IQMDYYWASY Y QSTAVPAG WLLALPFVRN YAHVRLIVPS KVGHSSAQQY VNPYYYDIWT FSKALN

UniProtKB: DUF4827 domain-containing protein

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Macromolecule #7: DUF4270 domain-containing protein

MacromoleculeName: DUF4270 domain-containing protein / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Molecular weightTheoretical: 58.264816 KDa
SequenceString: CDDNTGGLGL GMFPGNDQNI KGKLSTFDVT TESVKTGDIY AKTNIGYIGK FTDETFGTYQ AGFLAQLNCP DGLTFPEPYK EVTDASGNV ISATGRMVVD DKDPENKDVT FIKDGNQIIG NIRAVELYLW YDSYFGDSLT ACRLSVYELG GNGKETLNLD N AYYTDINP ...String:
CDDNTGGLGL GMFPGNDQNI KGKLSTFDVT TESVKTGDIY AKTNIGYIGK FTDETFGTYQ AGFLAQLNCP DGLTFPEPYK EVTDASGNV ISATGRMVVD DKDPENKDVT FIKDGNQIIG NIRAVELYLW YDSYFGDSLT ACRLSVYELG GNGKETLNLD N AYYTDINP EDFYDSQNIL GTKAYTAVDL SVKDSIRNLS TYVPSVHIAF KEDIATRVGG NILTAARKAK NADKEFNSQL FR EAFQGIY VKSDYGDGTV LYIDQPQMNV VYKCYATDSI TGKKLQKKDG SGKDSTYYSY RVFATTREVI QANQLKNDPE RID ALIKED KNTYLKSPAG IFTEATLPIS DIQNELTGDT LNAVKLTFTN YNQTGDKKFG MAIPSTVMLV RKKFQDSFFK DNKL SDGVS SYLTSHTSST NQYVFSNITK LVNACIAEKE EAKKNAGSSW DETKWLQENP DWNKVVLIPV LVTYDSSNTT TGQAN IIRI QHDLKPGYVR LKGGSLGKTN PDYKLKLEVI STDFGLTTKS N

UniProtKB: DUF4270 domain-containing protein

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Macromolecule #8: N-TRIDECANOIC ACID

MacromoleculeName: N-TRIDECANOIC ACID / type: ligand / ID: 8 / Number of copies: 1 / Formula: TDA
Molecular weightTheoretical: 214.344 Da
Chemical component information

ChemComp-TDA:
N-TRIDECANOIC ACID

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Macromolecule #9: (2S)-3-hydroxypropane-1,2-diyl dihexadecanoate

MacromoleculeName: (2S)-3-hydroxypropane-1,2-diyl dihexadecanoate / type: ligand / ID: 9 / Number of copies: 1 / Formula: Z41
Molecular weightTheoretical: 568.911 Da
Chemical component information

ChemComp-Z41:
(2S)-3-hydroxypropane-1,2-diyl dihexadecanoate

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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 correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Ab initio reconstruction
Final reconstructionNumber classes used: 2 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.46 Å / Resolution method: OTHER
Details: The best parts of two maps at 3.28 A and 3.46 A were combined using phenix.combine_focused_maps
Number images used: 105155
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Details: Non-uniform refinement

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Atomic model buiding 1

Initial model
PDB IDChain

9his

source_name: PDB, initial_model_type: experimental model

9hiv

source_name: PDB, initial_model_type: experimental model
DetailsExperimental models were fit into the combined focused map.
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 64.9
Output model

PDB-9hj3:
Bacteroides thetaiotaomicron BAM complex

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