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- EMDB-50740: CRYO-EM CONSENSUS MAP OF HCT15 VACANT 80S -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-50740
TitleCRYO-EM CONSENSUS MAP OF HCT15 VACANT 80S
Map dataConsensus map
Sample
  • Complex: HCT15 VACANT 80S
KeywordsCRYO-EM / HCT15 cancer / VACANT 80S / ribosome
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.85 Å
AuthorsRajan KS / Yonath A
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: CRYO-EM CONSENSUS MAP OF HCT15 VACANT 80S
Authors: Rajan KS / Yonath A
History
DepositionJun 23, 2024-
Header (metadata) releaseJul 2, 2025-
Map releaseJul 2, 2025-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50740.png

Downloads & links

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Map

FileDownload / File: emd_50740.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationConsensus map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.79 Å/pix.
x 480 pix.
= 380.64 Å		0.79 Å/pix.
x 480 pix.
= 380.64 Å		0.79 Å/pix.
x 480 pix.
= 380.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.793 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.005
Minimum - Maximum-0.0141047435 - 0.04663664
Average (Standard dev.)0.00023441567 (±0.0022980464)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 380.63998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map 2

Fileemd_50740_half_map_1.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1

Fileemd_50740_half_map_2.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : HCT15 VACANT 80S

EntireName: HCT15 VACANT 80S
Components
  • Complex: HCT15 VACANT 80S

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Supramolecule #1: HCT15 VACANT 80S

SupramoleculeName: HCT15 VACANT 80S / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)

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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: 7.6
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 1.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.7 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: PDB ENTRY
PDB model - PDB ID:

8glp

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.85 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 535236
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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