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- PDB-9hj3: Bacteroides thetaiotaomicron BAM complex -

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Basic information

Entry
Database: PDB / ID: 9hj3
TitleBacteroides thetaiotaomicron BAM complex
Components
  • (Outer membrane ...) x 2
  • DUF4270 domain-containing protein
  • DUF4827 domain-containing protein
  • DUF6242 domain-containing protein
  • Lipoprotein protein, putative
  • Peptidyl-prolyl cis-trans isomerase
KeywordsMEMBRANE PROTEIN / Outer membrane protein biogenesis / Beta-barrel assembly machinery / BAM
Function / homology
Function and homology information


membrane assembly / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / cell outer membrane
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) / 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) / 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
N-TRIDECANOIC ACID / (2S)-3-hydroxypropane-1,2-diyl dihexadecanoate / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.46 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: To be updated
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: Image / Data content type: Image / 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
A: Outer membrane protein
D: Lipoprotein protein, putative
F: Outer membrane protein
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)341,5579
Polymers340,7747
Non-polymers7832
Water00
1


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

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Components

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Outer membrane ... , 2 types, 2 molecules AF

#1: Protein Outer membrane protein


Mass: 101527.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Gene: BT_3725
Production host: Bacteroides thetaiotaomicron VPI-5482 (bacteria)
References: UniProt: Q8A1E1
#3: Protein Outer membrane protein


Mass: 47860.691 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacteroides thetaiotaomicron VPI-5482 (bacteria)
References: UniProt: Q89ZL0

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Protein , 5 types, 5 molecules DHIJG

#2: Protein Lipoprotein protein, putative


Mass: 31415.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacteroides thetaiotaomicron VPI-5482 (bacteria)
References: UniProt: Q8AA92
#4: 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
#5: 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
#6: 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
#7: 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

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


Mass: 214.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H26O2
#9: 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: Bacteroides thetaiotaomicron BAM complex / Type: COMPLEX / Entity ID: #1-#7 / Source: NATURAL
Molecular weightValue: 0.325 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: 3.46 Å / Resolution method: OTHER / Num. of particles: 105155 / Algorithm: FOURIER SPACE
Details: The best parts of two maps at 3.28 A and 3.46 A were combined using phenix.combine_focused_maps
Num. of class averages: 2 / Symmetry type: POINT
Atomic model buildingB value: 64.9 / Protocol: RIGID BODY FIT / Space: REAL
Details: Experimental models were fit into the combined focused map.
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
19HIS

9his

19HIS1PDBexperimental model
29HIV

9hiv

19HIV2PDBexperimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00619966
ELECTRON MICROSCOPYf_angle_d0.92427044
ELECTRON MICROSCOPYf_dihedral_angle_d8.0712723
ELECTRON MICROSCOPYf_chiral_restr0.0572914
ELECTRON MICROSCOPYf_plane_restr0.013487

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