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- EMDB-52200: Extracellular components BamHIJK of the Bacteroides thetaiotaomic... -

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Basic information

Entry
Database: EMDB / ID: EMD-52200
TitleExtracellular components BamHIJK of the Bacteroides thetaiotaomicron BAM machinery
Map dataunsharpened map
Sample
  • Complex: Extracellular components BamGHIJ of the Bacteroides thetaiotaomicron BAM complex
    • Protein or peptide: DUF4270 domain-containing protein
    • Protein or peptide: DUF6242 domain-containing protein
    • Protein or peptide: Peptidyl-prolyl cis-trans isomerase
    • Protein or peptide: DUF4827 domain-containing protein
  • Ligand: N-TRIDECANOIC ACID
  • Ligand: (2S)-3-hydroxypropane-1,2-diyl dihexadecanoate
KeywordsLipoproteins / Outer membrane protein biogenesis / Beta-barrel assembly machinery / BAM / MEMBRANE PROTEIN
Function / homology
Function and homology information


peptidylprolyl isomerase / 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) / 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
DUF4270 domain-containing protein / DUF4827 domain-containing protein / DUF6242 domain-containing protein / Peptidyl-prolyl cis-trans isomerase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron VPI-5482 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.28 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_52200.png

Downloads & links

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Map

FileDownload / File: emd_52200.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)

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: 0.0881
Minimum - Maximum-0.18528089 - 0.3909175
Average (Standard dev.)0.0010868156 (±0.01019823)
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_52200_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: sharpened map

Fileemd_52200_additional_1.map
Annotationsharpened map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_52200_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_52200_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Extracellular components BamGHIJ of the Bacteroides thetaiotaomic...

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

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Supramolecule #1: Extracellular components BamGHIJ of the Bacteroides thetaiotaomic...

SupramoleculeName: Extracellular components BamGHIJ of the Bacteroides thetaiotaomicron BAM complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #4, #1-#3
Source (natural)Organism: Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Molecular weightTheoretical: 153 KDa

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Macromolecule #1: DUF6242 domain-containing protein

MacromoleculeName: DUF6242 domain-containing protein / type: protein_or_peptide / ID: 1 / 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 #2: Peptidyl-prolyl cis-trans isomerase

MacromoleculeName: Peptidyl-prolyl cis-trans isomerase / type: protein_or_peptide / ID: 2 / 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 #3: DUF4827 domain-containing protein

MacromoleculeName: DUF4827 domain-containing protein / type: protein_or_peptide / ID: 3 / 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 #4: DUF4270 domain-containing protein

MacromoleculeName: DUF4270 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: 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 #5: N-TRIDECANOIC ACID

MacromoleculeName: N-TRIDECANOIC ACID / type: ligand / ID: 5 / Number of copies: 1 / Formula: TDA
Molecular weightTheoretical: 214.344 Da
Chemical component information

ChemComp-TDA:
N-TRIDECANOIC ACID

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Macromolecule #6: (2S)-3-hydroxypropane-1,2-diyl dihexadecanoate

MacromoleculeName: (2S)-3-hydroxypropane-1,2-diyl dihexadecanoate / type: ligand / ID: 6 / 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: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 48834
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Details: Non-uniform refinement
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

7-f1

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

2-f1

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

9-f1

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

0-f1

chain_id: G, source_name: AlphaFold, initial_model_type: in silico model
DetailsAlphaFold2 models were docked using Phenix.
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 58
Output model

PDB-9his:
Extracellular components BamHIJK of the Bacteroides thetaiotaomicron BAM machinery

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