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- EMDB-71133: Focused refinement of beta-barrel assembly machine from Escherich... -

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Basic information

Entry
Database: EMDB / ID: EMD-71133
TitleFocused refinement of beta-barrel assembly machine from Escherichia coli in an late state of LptD assembly
Map dataLocal refinement map
Sample
  • Complex: Late intermediate state of folding of LptD on the beta-barrel assembly machine
Keywordsbeta-barrel assembly machine / outer membrane / folding intermediate / MEMBRANE PROTEIN
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsThomson BD / Marquez MD / 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: Proc Natl Acad Sci U S A / Year: 2026
Title: Structures of folding intermediates on BAM show diverse substrates fold by a conserved mechanism.
Authors: Benjamin D Thomson / Melissa D Marquez / Shaun Rawson / Thiago M A Dos Santos / Stephen C Harrison / Daniel Kahne /
Abstract: The outer membranes of mitochondria, chloroplasts, and Gram-negative bacteria contain β-barrel membrane proteins that are assembled by conserved multisubunit machines. In bacteria, the β-barrel ...The outer membranes of mitochondria, chloroplasts, and Gram-negative bacteria contain β-barrel membrane proteins that are assembled by conserved multisubunit machines. In bacteria, the β-barrel assembly machine (BAM) folds over a hundred compositionally different substrates into barrels that vary greatly in size. Some larger barrels require globular proteins to plug the barrel lumen. How a single machine can assemble such different barrels is unknown. Here we report three structures representing progressively folded stages of a 16-stranded barrel engaged with BAM, as well as the structure of a late-stage folding intermediate of a 26-stranded substrate folding around its soluble lipoprotein plug on BAM. We find that BAM catalyzes folding of these substrates by a uniform mechanism in which BAM undergoes major distortions to accommodate the nascent barrel.
History
DepositionJun 10, 2025-
Header (metadata) releaseMar 25, 2026-
Map releaseMar 25, 2026-
UpdateApr 15, 2026-
Current statusApr 15, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71133.png

Downloads & links

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Map

FileDownload / File: emd_71133.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocal refinement map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.74 Å/pix.
x 440 pix.
= 323.84 Å		0.74 Å/pix.
x 440 pix.
= 323.84 Å		0.74 Å/pix.
x 440 pix.
= 323.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.736 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.019
Minimum - Maximum-0.060885113 - 0.12008713
Average (Standard dev.)0.00019849023 (±0.002942759)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 323.84 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Local refinement half map A

Fileemd_71133_half_map_1.map
AnnotationLocal refinement half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Local refinement half map B

Fileemd_71133_half_map_2.map
AnnotationLocal refinement half 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 : Late intermediate state of folding of LptD on the beta-barrel ass...

EntireName: Late intermediate state of folding of LptD on the beta-barrel assembly machine
Components
  • Complex: Late intermediate state of folding of LptD on the beta-barrel assembly machine

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Supramolecule #1: Late intermediate state of folding of LptD on the beta-barrel ass...

SupramoleculeName: Late intermediate state of folding of LptD on the beta-barrel assembly machine
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 320 KDa

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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

Concentration1.5 mg/mL
BufferpH: 8
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
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: TFS FALCON 4i (4k x 4k) / Average electron dose: 49.55 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: 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: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 79819
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

5lj0

source_name: PDB, initial_model_type: experimental model
source_name: AlphaFold, initial_model_type: in silico model

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