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- EMDB-42834: Cryo-EM maps of the NCP-RCC1-Ran complex with multiple binding states -

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Basic information

Entry
Database: EMDB / ID: EMD-42834
TitleCryo-EM maps of the NCP-RCC1-Ran complex with multiple binding states
Map dataLocal sharpened map of RCC1-Ran bound to one side of NCP
Sample
  • Complex: Ran-RCC1-NCP complex
KeywordsGTPase / Guanine nucleotide exchange factor / chromatin-binding / NUCLEAR PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.43 Å
AuthorsHuang SK / Rubinstein JL / Kay LE
Funding support Canada, 2 items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)2015-04347 Canada
Canadian Institutes of Health Research (CIHR)FND-50357 Canada
CitationJournal: To Be Published
Title: Structure of Ran bound to RCC1 and the nucleosome core particle
Authors: Huang SK / Rubinstein JL / Kay LE
History
DepositionNov 14, 2023-
Header (metadata) releaseNov 22, 2023-
Map releaseNov 22, 2023-
UpdateNov 22, 2023-
Current statusNov 22, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42834.png

Downloads & links

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Map

FileDownload / File: emd_42834.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocal sharpened map of RCC1-Ran bound to one side of NCP
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 256 pix.
= 263.68 Å		1.03 Å/pix.
x 256 pix.
= 263.68 Å		1.03 Å/pix.
x 256 pix.
= 263.68 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.03 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-0.068406686 - 6.309859
Average (Standard dev.)0.006349486 (±0.12227844)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 263.68 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Unsharpened map of a free NCP without RCC1 or Ran bound

Fileemd_42834_additional_1.map
AnnotationUnsharpened map of a free NCP without RCC1 or Ran bound
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened map of RCC1-Ran bound to both sides of NCP

Fileemd_42834_additional_2.map
AnnotationUnsharpened map of RCC1-Ran bound to both sides of NCP
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened map of RCC1-Ran bound to one side of NCP

Fileemd_42834_additional_3.map
AnnotationUnsharpened map of RCC1-Ran bound to one side of NCP
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened map of RCC1-Ran bound to one side...

Fileemd_42834_additional_4.map
AnnotationUnsharpened map of RCC1-Ran bound to one side of NCP and only RCC1 (no Ran) bound to the other side of NCP
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened map of RCC1 bound to both sides of NCP

Fileemd_42834_additional_5.map
AnnotationUnsharpened map of RCC1 bound to both sides of NCP
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened map of RCC1 bound to one side of NCP

Fileemd_42834_additional_6.map
AnnotationUnsharpened map of RCC1 bound to one side of NCP
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A of RCC1-Ran bound to one side of NCP

Fileemd_42834_half_map_1.map
AnnotationHalf map A of RCC1-Ran bound to one side of NCP
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B of RCC1-Ran bound to one side of NCP

Fileemd_42834_half_map_2.map
AnnotationHalf map B of RCC1-Ran bound to one side of NCP
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Ran-RCC1-NCP complex

EntireName: Ran-RCC1-NCP complex
Components
  • Complex: Ran-RCC1-NCP complex

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Supramolecule #1: Ran-RCC1-NCP complex

SupramoleculeName: Ran-RCC1-NCP complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.43 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 199434
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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