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- EMDB-54535: Cryo-EM map of the E. coli 50S ribosomal subunit -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-54535
TitleCryo-EM map of the E. coli 50S ribosomal subunit
Map dataCryo-EM map of the E. coli 50S ribosomal subunit
Sample
  • Complex: E. coli strain MRE600
Keywords50S / E. Coli / RIBOSOME
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 20.0 Å
AuthorsBron P / Lai-Kee-Him J
Funding support1 items
OrganizationGrant numberCountry
Other government
CitationJournal: To Be Published
Title: Cryo-EM map of the E. coli 50S ribosomal subunit
Authors: Bron P / Lai-Kee-Him J
History
DepositionJul 24, 2025-
Header (metadata) releaseAug 12, 2026-
Map releaseAug 12, 2026-
UpdateAug 12, 2026-
Current statusAug 12, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54535.png

Downloads & links

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Map

FileDownload / File: emd_54535.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of the E. coli 50S ribosomal subunit
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.1 Å/pix.
x 180 pix.
= 378. Å		2.1 Å/pix.
x 180 pix.
= 378. Å		2.1 Å/pix.
x 180 pix.
= 378. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0424
Minimum - Maximum-0.035773568 - 0.13082482
Average (Standard dev.)-0.00018157442 (±0.016980678)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 377.99997 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : E. coli strain MRE600

EntireName: E. coli strain MRE600
Components
  • Complex: E. coli strain MRE600

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Supramolecule #1: E. coli strain MRE600

SupramoleculeName: E. coli strain MRE600 / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Escherichia coli (E. coli)

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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: 7.5
GridModel: Quantifoil R2/2 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: GATAN CRYOPLUNGE 3

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Electron microscopy

MicroscopeJEOL 2200FS
Specialist opticsEnergy filter - Name: In-column Omega Filter / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN ORIUS SC200 (2k x 2k) / Average electron dose: 18.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.4000000000000001 µm / Nominal magnification: 50000
Sample stageSpecimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Cooling holder cryogen: NITROGEN

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Image processing

CTF correctionSoftware - Name: IMAGIC / Type: PHASE FLIPPING ONLY
Startup modelType of model: EMDB MAP
EMDB ID:

1006

Final reconstructionResolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IMAGIC / Number images used: 1459
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: IMAGIC
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: IMAGIC

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