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- EMDB-54478: LolCDE LolE R239C Y250C mutant closed conformation -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-54478
TitleLolCDE LolE R239C Y250C mutant closed conformation
Map data
Sample
  • Complex: LolCDE LolE R239C Y250C mutant closed conformation
KeywordsGram-negative / envelope biogenesis / outer membrane protein / PROTEIN TRANSPORT
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.26 Å
AuthorsSymmons MF / Szewczyk P / Greene NP / Hardwick SW / Koronakis V
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/V000616/1 United Kingdom
CitationJournal: To Be Published
Title: LolCDE LolE R239C Y250C mutant closed conformation
Authors: Symmons MF / Szewczyk P / Greene NP / Koronakis V
History
DepositionJul 21, 2025-
Header (metadata) releaseJan 21, 2026-
Map releaseJan 21, 2026-
UpdateJan 21, 2026-
Current statusJan 21, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54478.png

Downloads & links

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Map

FileDownload / File: emd_54478.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.73 Å/pix.
x 384 pix.
= 279.936 Å		0.73 Å/pix.
x 384 pix.
= 279.936 Å		0.73 Å/pix.
x 384 pix.
= 279.936 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.729 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.25577462 - 0.5632245
Average (Standard dev.)0.00014114451 (±0.011095913)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 279.93597 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_54478_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_54478_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : LolCDE LolE R239C Y250C mutant closed conformation

EntireName: LolCDE LolE R239C Y250C mutant closed conformation
Components
  • Complex: LolCDE LolE R239C Y250C mutant closed conformation

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Supramolecule #1: LolCDE LolE R239C Y250C mutant closed conformation

SupramoleculeName: LolCDE LolE R239C Y250C mutant closed conformation / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Escherichia coli (E. coli) / Strain: K12

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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

BufferpH: 8
VitrificationCryogen name: ETHANE / 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: 52.45 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: 0.8 µm / Nominal magnification: 165000
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: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.26 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 92720
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: in silico model / Details: Composite from PDB entries
RefinementSpace: REAL / Protocol: FLEXIBLE FIT

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