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- PDB-9n2f: Cryo-EM structure of F. johnsoniae BamAD -

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Basic information

Entry
Database: PDB / ID: 9n2f
TitleCryo-EM structure of F. johnsoniae BamAD
Components
  • DNA uptake lipoprotein-like protein
  • Surface antigen (D15)
KeywordsMEMBRANE PROTEIN / BAM complex / BamA / BamD / outer-membrane proteins / OMP
Function / homology
Function and homology information


membrane assembly / cell outer membrane
Similarity search - Function
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 / POTRA domain / POTRA domain profile. / Bacterial surface antigen (D15) / Omp85 superfamily domain ...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 / POTRA domain / POTRA domain profile. / Bacterial surface antigen (D15) / Omp85 superfamily domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
DNA uptake lipoprotein-like protein / Surface antigen (D15)
Similarity search - Component
Biological speciesFlavobacterium johnsoniae UW101 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 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 16, 2025Provider: repository / Type: Initial release
Revision 1.0Jul 16, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
F: DNA uptake lipoprotein-like protein
A: Surface antigen (D15)


Theoretical massNumber of molelcules
Total (without water)131,7102
Polymers131,7102
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 DNA uptake lipoprotein-like protein


Mass: 30219.377 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: A5FE81
#2: 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
Has ligand of interestN
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: BamAD complex / Type: COMPLEX / Entity ID: #1 / 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: 52 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1SIMPLEparticle selection
2PHENIXdev_5533model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 534368 / Symmetry type: POINT
RefinementHighest resolution: 3.5 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0037775
ELECTRON MICROSCOPYf_angle_d0.64210494
ELECTRON MICROSCOPYf_dihedral_angle_d7.1661093
ELECTRON MICROSCOPYf_chiral_restr0.0461099
ELECTRON MICROSCOPYf_plane_restr0.0041360

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