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- PDB-9his: Extracellular components BamHIJK of the Bacteroides thetaiotaomic... -

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Basic information

Entry
Database: PDB / ID: 9his
TitleExtracellular components BamHIJK of the Bacteroides thetaiotaomicron BAM machinery
Components
  • DUF4270 domain-containing protein
  • DUF4827 domain-containing protein
  • DUF6242 domain-containing protein
  • Peptidyl-prolyl cis-trans isomerase
KeywordsMEMBRANE PROTEIN / Lipoproteins / Outer membrane protein biogenesis / Beta-barrel assembly machinery / BAM
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) / 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
N-TRIDECANOIC ACID / (2S)-3-hydroxypropane-1,2-diyl dihexadecanoate / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.28 Å
AuthorsSilale, A. / van den Berg, B.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust214222/Z/18/Z United Kingdom
CitationJournal: To Be Published
Title: Extracellular components BamGHIJ of the Bacteroides thetaiotaomicron BAM machinery
Authors: Silale, A. / van den Berg, B.
History
DepositionNov 27, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 27, 2025Provider: repository / Type: Initial release
Revision 1.0Aug 27, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 27, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Aug 27, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Aug 27, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 27, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 27, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 27, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Aug 27, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: DUF6242 domain-containing protein
I: Peptidyl-prolyl cis-trans isomerase
J: DUF4827 domain-containing protein
G: DUF4270 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,7536
Polymers159,9704
Non-polymers7832
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 , 4 types, 4 molecules HIJG

#1: Protein DUF6242 domain-containing protein


Mass: 55108.051 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacteroides thetaiotaomicron VPI-5482 (bacteria)
References: UniProt: Q8A1D9
#2: Protein Peptidyl-prolyl cis-trans isomerase


Mass: 21884.557 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacteroides thetaiotaomicron VPI-5482 (bacteria)
References: UniProt: Q8A1P7, peptidylprolyl isomerase
#3: Protein DUF4827 domain-containing protein


Mass: 24712.709 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacteroides thetaiotaomicron VPI-5482 (bacteria)
References: UniProt: Q8A0S2
#4: Protein DUF4270 domain-containing protein


Mass: 58264.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacteroides thetaiotaomicron VPI-5482 (bacteria)
References: UniProt: Q89ZS0

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Non-polymers , 2 types, 2 molecules

#5: Chemical ChemComp-TDA / N-TRIDECANOIC ACID


Mass: 214.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H26O2
#6: 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: Extracellular components BamGHIJ of the Bacteroides thetaiotaomicron BAM complex
Type: COMPLEX / Entity ID: #4, #1-#3 / Source: NATURAL
Molecular weightValue: 0.153 MDa / Experimental value: NO
Source (natural)Organism: Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mMsodium chlorideNaCl1
210 mMHEPESHEPES1
30.04 %dodecyl maltosideDDM1
SpecimenConc.: 8 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 R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / 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: 165000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 35 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 13558
EM imaging opticsEnergyfilter name: TFS Selectris / Energyfilter slit width: 10 eV

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2266553
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 48834 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 58 / Protocol: RIGID BODY FIT / Space: REAL / Details: AlphaFold2 models were docked using Phenix.
Atomic model building
ID 3D fitting-IDAccession codeChain-IDInitial refinement model-IDSource nameType
11AF-Q8A1P7-F1I1AlphaFoldin silico model
21AF-Q8A0S2-F1J2AlphaFoldin silico model
31AF-Q8A1D9-F1H3AlphaFoldin silico model
41AF-Q89ZS0-F1G4AlphaFoldin silico model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00410739
ELECTRON MICROSCOPYf_angle_d0.78814570
ELECTRON MICROSCOPYf_dihedral_angle_d9.0221472
ELECTRON MICROSCOPYf_chiral_restr0.0531614
ELECTRON MICROSCOPYf_plane_restr0.0051876

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