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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: To Be Published
Title: An extended BAM complex in the Bacteroidota
Authors: Liu, X. / Orenday Tapia, L. / Deme, J.C. / Lea, S.M. / Berks, B.C.
History
DepositionJan 28, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2025Provider: repository / Type: Initial release
Revision 1.0Jul 9, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 9, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
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Revision 1.0Jul 9, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 9, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
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Revision 1.0Jul 9, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
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Revision 1.0Jul 9, 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

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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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