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- PDB-9n2e: Cryo-EM structure of F. johnsoniae BamAP -

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Basic information

Entry
Database: PDB / ID: 9n2e
TitleCryo-EM structure of F. johnsoniae BamAP
Components
  • CarboxypepD_reg-like domain-containing protein
  • Surface antigen (D15)
KeywordsMEMBRANE PROTEIN / BamAP complex / BamA / BamP / outer-membrane proteins / OMP
Function / homology
Function and homology information


membrane assembly / cell outer membrane
Similarity search - Function
Outer membrane protein assembly factor BamA / POTRA domain, BamA/TamA-like / Surface antigen variable number repeat / POTRA domain / POTRA domain profile. / Bacterial surface antigen (D15) / Omp85 superfamily domain
Similarity search - Domain/homology
CarboxypepD_reg-like domain-containing protein / Surface antigen (D15)
Similarity search - Component
Biological speciesFlavobacterium johnsoniae UW101 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsDeme, J.C. / Lea, S.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CCR Core Funding for Lea Group United States
CitationJournal: Nat Commun / Year: 2025
Title: A shared mechanism for Bacteroidota protein transport and gliding motility.
Authors: Xiaolong Liu / Marieta Avramova / Justin C Deme / Rachel L Jones / Camilla A K Lundgren / Susan M Lea / Ben C Berks /
Abstract: Bacteria of the phylum Bacteroidota are major human commensals and pathogens in addition to being abundant members of the wider biosphere. Bacteroidota move by gliding and they export proteins using ...Bacteria of the phylum Bacteroidota are major human commensals and pathogens in addition to being abundant members of the wider biosphere. Bacteroidota move by gliding and they export proteins using the Type 9 Secretion System (T9SS). Here we discover that gliding motility and the T9SS share an unprecedented mechanism of energisation in which outer membrane proteins are covalently attached by disulfide bonds to a moving internal track structure that propels them laterally through the membrane. We determined the structure of an exemplar Bacteroidota mobile track by obtaining the cryoEM structure of a 3 MDa circular mini-track from Porphyromonas gingivalis. Our discoveries identify a mechanistic and evolutionary link between gliding motility and T9SS-dependent protein transport.
History
DepositionJan 28, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2025Provider: repository / Type: Initial release
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Revision 1.1Jan 21, 2026Group: Data collection / Database references / Structure summary
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Surface antigen (D15)
E: CarboxypepD_reg-like domain-containing protein


Theoretical massNumber of molelcules
Total (without water)129,9042
Polymers129,9042
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 Surface antigen (D15)


Mass: 101490.320 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Flavobacterium johnsoniae UW101 (bacteria)
Strain: ATCC 17061 / DSM 2064 / JCM 8514 / BCRC 14874 / CCUG 350202 / NBRC 14942 / NCIMB 11054 / UW101
References: UniProt: A5FJ90
#2: Protein CarboxypepD_reg-like domain-containing protein


Mass: 28413.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Flavobacterium johnsoniae UW101 (bacteria)
Strain: ATCC 17061 / DSM 2064 / JCM 8514 / BCRC 14874 / CCUG 350202 / NBRC 14942 / NCIMB 11054 / UW101
References: UniProt: A5FJ21
Has protein modificationN

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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: BamAP complex / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Flavobacterium johnsoniae UW101 (bacteria)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: 2500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 55.7 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: dev_5533 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 96076 / Symmetry type: POINT
RefinementHighest resolution: 3.7 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0035039
ELECTRON MICROSCOPYf_angle_d0.6116798
ELECTRON MICROSCOPYf_dihedral_angle_d8.33708
ELECTRON MICROSCOPYf_chiral_restr0.045711
ELECTRON MICROSCOPYf_plane_restr0.004881

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