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- PDB-9ccg: Fusobacterium nucleatum BamA-Fab 9 complex -

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Basic information

Entry
Database: PDB / ID: 9ccg
TitleFusobacterium nucleatum BamA-Fab 9 complex
Components
  • Fab 9 heavy chain
  • Fab 9 light chain
  • POTRA domain-containing protein
KeywordsMEMBRANE PROTEIN / proteomics / protein folding / structural biology
Function / homologyPOTRA 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 / cell outer membrane / POTRA domain-containing protein
Function and homology information
Biological speciesFusobacterium nucleatum (bacteria)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.87 Å
AuthorsOverly Cottom, C. / Noinaj, N.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM127884 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM127896 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R01AI127793 United States
CitationJournal: Structure / Year: 2025
Title: Characterization of the OMP biogenesis machinery in Fusobacterium nucleatum.
Authors: Claire Overly Cottom / Eva Heinz / Satchal Erramilli / Anthony Kossiakoff / Daniel J Slade / Nicholas Noinaj /
Abstract: F. nucleatum is a Gram-negative bacteria that causes oral infections and is linked to colorectal cancer. Pathogenicity relies on a type of β-barrel outer membrane protein (OMP) called an ...F. nucleatum is a Gram-negative bacteria that causes oral infections and is linked to colorectal cancer. Pathogenicity relies on a type of β-barrel outer membrane protein (OMP) called an autotransporter. The biogenesis of OMPs is typically mediated by the barrel assembly machinery (BAM) complex. In this study, we investigate the evolution, composition, and structure of the OMP biogenesis machinery in F. nucleatum. Our bioinformatics and proteomics analyses indicate that OMP biogenesis in F. nucleatum is mediated solely by the core component BamA. The structure of FnBamA highlights distinct features, including four POTRA domains and a C-terminal 16-stranded β-barrel domain observed as an inverted dimer. FnBamA represents the original composition of the assembly machinery, and a duplication event that resulted in BamA and TamA occurred after the split of other lineages, including the Proteobacteria, from the Fusobacteria. FnBamA, therefore, likely serves a singular role in the biogenesis of all OMPs.
History
DepositionJun 21, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 17, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: POTRA domain-containing protein
B: Fab 9 heavy chain
C: Fab 9 light chain
D: POTRA domain-containing protein
E: Fab 9 light chain
F: Fab 9 heavy chain


Theoretical massNumber of molelcules
Total (without water)246,7166
Polymers246,7166
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein POTRA domain-containing protein


Mass: 75980.375 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fusobacterium nucleatum (bacteria) / Gene: RO03_10440 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A101K5E7
#2: Antibody Fab 9 heavy chain


Mass: 24276.992 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#3: Antibody Fab 9 light chain


Mass: 23100.695 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
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: FnBamA-Fab9 complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 121 kDa/nm / Experimental value: YES
Source (natural)Organism: Fusobacterium nucleatum (bacteria) / Strain: ATCC 23726
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21 / Plasmid: pHIS2
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMTris buffer, pH 7.6Tris-Cl1
2150 mMsodium chlorideNaCl1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was monodisperse
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN 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: 57.8 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: classification
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.87 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 168664 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00317349
ELECTRON MICROSCOPYf_angle_d0.59623533
ELECTRON MICROSCOPYf_dihedral_angle_d13.5752412
ELECTRON MICROSCOPYf_chiral_restr0.0432600
ELECTRON MICROSCOPYf_plane_restr0.0043031

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