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- PDB-9p1u: beta-barrel assembly machine from Escherichia coli in an late sta... -

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Basic information

Entry
Database: PDB / ID: 9p1u
Titlebeta-barrel assembly machine from Escherichia coli in an late state of LptD assembly
Components
  • (LPS-assembly ...) x 2
  • (Outer membrane protein assembly factor ...) x 5
KeywordsMEMBRANE PROTEIN / beta-barrel assembly machine / outer membrane / folding intermediate
Function / homology
Function and homology information


transporter complex / lipopolysaccharide transport / Bam protein complex / Gram-negative-bacterium-type cell outer membrane assembly / Secretion of toxins / protein insertion into membrane / cell outer membrane / lipopolysaccharide binding / protein-macromolecule adaptor activity / cell adhesion ...transporter complex / lipopolysaccharide transport / Bam protein complex / Gram-negative-bacterium-type cell outer membrane assembly / Secretion of toxins / protein insertion into membrane / cell outer membrane / lipopolysaccharide binding / protein-macromolecule adaptor activity / cell adhesion / response to antibiotic / cell surface / membrane / identical protein binding
Similarity search - Function
LptD, C-terminal / LPS-assembly protein LptD / : / LPS transport system D / LPS-assembly lipoprotein LptE / Lipopolysaccharide-assembly / Organic solvent tolerance-like, N-terminal / LptA/(LptD N-terminal domain) LPS transport protein / Outer membrane protein assembly factor BamB / Outer membrane protein assembly factor BamC ...LptD, C-terminal / LPS-assembly protein LptD / : / LPS transport system D / LPS-assembly lipoprotein LptE / Lipopolysaccharide-assembly / Organic solvent tolerance-like, N-terminal / LptA/(LptD N-terminal domain) LPS transport protein / Outer membrane protein assembly factor BamB / Outer membrane protein assembly factor BamC / NlpB/DapX lipoprotein / Outer membrane protein assembly factor BamC, C-terminal / NlpB/DapX lipoprotein / Outer membrane protein assembly factor BamB / Outer membrane protein assembly factor BamE / Lipoprotein SmpA/OmlA / Outer membrane protein assembly factor BamE domain / Outer membrane protein assembly factor BamD / Outer membrane lipoprotein BamD-like / Outer membrane lipoprotein / BamE-like / Pyrrolo-quinoline quinone repeat / Outer membrane protein assembly factor BamA / POTRA domain, BamA/TamA-like / Surface antigen variable number repeat / Surface antigen D15-like / Pyrrolo-quinoline quinone beta-propeller repeat / beta-propeller repeat / POTRA domain / POTRA domain profile. / Bacterial surface antigen (D15) / Omp85 superfamily domain / Quinoprotein alcohol dehydrogenase-like superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Tetratricopeptide-like helical domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Outer membrane protein assembly factor BamC / Outer membrane protein assembly factor BamE / Outer membrane protein assembly factor BamA / Outer membrane protein assembly factor BamD / LPS-assembly lipoprotein LptE / LPS-assembly protein LptD / Outer membrane protein assembly factor BamB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsThomson, B.D. / Marquez, M.D. / Kahne, D.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI081059 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19AI158028 United States
CitationJournal: Biorxiv / Year: 2025
Title: Structures of folding intermediates on BAM show diverse substrates fold by a uniform mechanism
Authors: Thomson, B.D. / Marquez, M.D. / Rawson, S. / dos Santos, T.M.A. / Harrison, S.C. / Kahne, D.
History
DepositionJun 10, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data 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
C: Outer membrane protein assembly factor BamC
D: Outer membrane protein assembly factor BamD
E: Outer membrane protein assembly factor BamE
G: LPS-assembly lipoprotein LptE
F: LPS-assembly protein LptD
B: Outer membrane protein assembly factor BamB
A: Outer membrane protein assembly factor BamA


Theoretical massNumber of molelcules
Total (without water)325,1457
Polymers325,1457
Non-polymers00
Water00
1


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

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Components

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Outer membrane protein assembly factor ... , 5 types, 5 molecules CDEBA

#1: Protein Outer membrane protein assembly factor BamC


Mass: 36875.277 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: bamC, dapX, nlpB, b2477, JW2462 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A903
#2: Protein Outer membrane protein assembly factor BamD


Mass: 27858.350 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: bamD, yfiO, b2595, JW2577 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AC02
#3: Protein Outer membrane protein assembly factor BamE


Mass: 12310.977 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: bamE, smpA, b2617, JW2598 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A937
#6: Protein Outer membrane protein assembly factor BamB


Mass: 41918.945 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: bamB, yfgL, b2512, JW2496 / Production host: Escherichia coli (E. coli) / References: UniProt: P77774
#7: Protein Outer membrane protein assembly factor BamA / Omp85


Mass: 91736.602 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: bamA, yaeT, yzzN, yzzY, b0177, JW0172 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A940

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LPS-assembly ... , 2 types, 2 molecules GF

#4: Protein LPS-assembly lipoprotein LptE / Rare lipoprotein B


Mass: 21381.527 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: lptE, rlpB, b0641, JW0636 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ADC1
#5: Protein LPS-assembly protein LptD / Organic solvent tolerance protein


Mass: 93063.148 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: lptD, imp, ostA, yabG, b0054, JW0053 / Production host: Escherichia coli (E. coli) / References: UniProt: P31554

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Details

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: Late intermediate state of folding of LptD on the beta-barrel assembly machine
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.32 MDa / Experimental value: YES
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenConc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R2/1
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 defocus max: 2000 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 49.55 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

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Processing

EM software
IDNameVersionCategory
10cryoSPARCfinal Euler assignment
12cryoSPARC3D reconstruction
13PHENIX1.20.1_4487model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 79819 / Symmetry type: POINT
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
15LJ0

5lj0

15LJ01PDBexperimental model
21AlphaFoldin silico model
RefinementHighest resolution: 4.1 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00416192
ELECTRON MICROSCOPYf_angle_d0.85121935
ELECTRON MICROSCOPYf_dihedral_angle_d7.172283
ELECTRON MICROSCOPYf_chiral_restr0.0472283
ELECTRON MICROSCOPYf_plane_restr0.0062936

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