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- EMDB-32076: The cryo-EM map of the U1 region of human pre-A complex -

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Basic information

Entry
Database: EMDB / ID: EMD-32076
TitleThe cryo-EM map of the U1 region of human pre-A complex
Map dataThe U1 region of human pre-A complex
Sample
  • Complex: human pre-A complex
Keywordshuman spliceosome / pre-A complex / PRP5 / A complex / U1 snRNP / U2 snRNP / SPLICING
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 15.0 Å
AuthorsZhang X / Zhan X / Shi Y
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2024
Title: Structural insights into branch site proofreading by human spliceosome
Authors: Zhang X / Zhan X / Bian T / Yang F / Li P / Lu Y / Xing Z / Fan R / Zhang QC / Shi Y
History
DepositionOct 18, 2021-
Header (metadata) releaseOct 26, 2022-
Map releaseOct 26, 2022-
UpdateJan 17, 2024-
Current statusJan 17, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32076.png

Downloads & links

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Map

FileDownload / File: emd_32076.map.gz / Format: CCP4 / Size: 35.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe U1 region of human pre-A complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.17 Å/pix.
x 210 pix.
= 456.54 Å		2.17 Å/pix.
x 210 pix.
= 456.54 Å		2.17 Å/pix.
x 210 pix.
= 456.54 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.174 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.01737503 - 0.06832991
Average (Standard dev.)0.00010371959 (±0.003280285)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions210210210
Spacing210210210
CellA=B=C: 456.54 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : human pre-A complex

EntireName: human pre-A complex
Components
  • Complex: human pre-A complex

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Supramolecule #1: human pre-A complex

SupramoleculeName: human pre-A complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#34
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: 7.9
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
Final reconstructionResolution.type: BY AUTHOR / Resolution: 15.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 310889
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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