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- EMDB-48251: Consensus refinement of the barrel region of beta-barrel assembly... -

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Basic information

Entry
Database: EMDB / ID: EMD-48251
TitleConsensus refinement of the barrel region of beta-barrel assembly machine from Escherichia coli in an late state of substrate assembly
Map dataConsensus refinement of the barrel region of beta-barrel assembly machine from Escherichia coli in an late state of substrate assembly
Sample
  • Complex: BamABCDE bound to BamA substrate in a late folding intermediate state
Keywordsbeta-barrel assembly machine / outer membrane / folding intermediate / MEMBRANE PROTEIN
Biological speciesEscherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsThomson BD / Kahne D
Funding support United States, 2 items
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 BD / Marquez MD / Rawson S / dos Santos TMA / Harrison SC / Kahne D
History
DepositionDec 10, 2024-
Header (metadata) releaseDec 17, 2025-
Map releaseDec 17, 2025-
UpdateDec 17, 2025-
Current statusDec 17, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48251.png

Downloads & links

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Map

FileDownload / File: emd_48251.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationConsensus refinement of the barrel region of beta-barrel assembly machine from Escherichia coli in an late state of substrate assembly
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 320 pix.
= 265.6 Å		0.83 Å/pix.
x 320 pix.
= 265.6 Å		0.83 Å/pix.
x 320 pix.
= 265.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.022
Minimum - Maximum-0.11161463 - 0.1589839
Average (Standard dev.)0.000061651364 (±0.004071647)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 265.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map A

Fileemd_48251_half_map_1.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_48251_half_map_2.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : BamABCDE bound to BamA substrate in a late folding intermediate state

EntireName: BamABCDE bound to BamA substrate in a late folding intermediate state
Components
  • Complex: BamABCDE bound to BamA substrate in a late folding intermediate state

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Supramolecule #1: BamABCDE bound to BamA substrate in a late folding intermediate state

SupramoleculeName: BamABCDE bound to BamA substrate in a late folding intermediate state
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Escherichia coli K-12 (bacteria)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMTris-HClTris(hydroxymethyl)aminomethane hydrochloride
150.0 mMNaClSodium chloride
0.004 %GDNGlyco-diosgenin
GridModel: Quantifoil R2/1 / Material: COPPER / Support film - Material: GOLD
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 21962 / Average exposure time: 2.5 sec. / Average electron dose: 49.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Details: Ab-initio model generated within cryoSPARC based on the data
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 36580
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

5d0o

source_name: PDB, initial_model_type: experimental model

5d0q

source_name: PDB, initial_model_type: experimental model

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