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- EMDB-10611: Cryo-EM map of DDB1:DCAF:Vpr State 1 -

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Basic information

Entry
Database: EMDB / ID: EMD-10611
TitleCryo-EM map of DDB1:DCAF:Vpr State 1
Map dataCryo-EM map of DDB1:DCAF:Vpr State 1
Sample
  • Complex: Cryo-EM map of DDB1:DCAF:Vpr State 1
Biological speciesSpodoptera frugiperda (fall armyworm)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.5 Å
AuthorsKrupp F / Banchenko S / Buerger J / Mielke T / Spahn CMT / Schwefel D
Funding support Germany, 3 items
OrganizationGrant numberCountry
German Research Foundation (DFG)25065445 Germany
European Molecular Biology Organization (EMBO)190-2016 Germany
German Research Foundation (DFG)Emmy Noether Programme 280022178 Germany
CitationJournal: To Be Published
Title: Cryo-EM map of DDB1:DCAF:Vpr State 1
Authors: Krupp F / Banchenko S / Buerger J / Mielke T / Spahn CMT / Schwefel D
History
DepositionJan 15, 2020-
Header (metadata) releaseJan 27, 2021-
Map releaseJan 27, 2021-
UpdateApr 14, 2021-
Current statusApr 14, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.018
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.018
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10611.png

Downloads & links

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Map

FileDownload / File: emd_10611.map.gz / Format: CCP4 / Size: 59.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of DDB1:DCAF:Vpr State 1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.25 Å/pix.
x 250 pix.
= 312.5 Å		1.25 Å/pix.
x 250 pix.
= 312.5 Å		1.25 Å/pix.
x 250 pix.
= 312.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.25 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.018 / Movie #1: 0.018
Minimum - Maximum-0.06612629 - 0.09713697
Average (Standard dev.)9.9168e-05 (±0.002736384)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions250250250
Spacing250250250
CellA=B=C: 312.5 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.251.251.25
M x/y/z250250250
origin x/y/z0.0000.0000.000
length x/y/z312.500312.500312.500
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS250250250
D min/max/mean-0.0660.0970.000

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Supplemental data

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Sample components

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Entire : Cryo-EM map of DDB1:DCAF:Vpr State 1

EntireName: Cryo-EM map of DDB1:DCAF:Vpr State 1
Components
  • Complex: Cryo-EM map of DDB1:DCAF:Vpr State 1

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Supramolecule #1: Cryo-EM map of DDB1:DCAF:Vpr State 1

SupramoleculeName: Cryo-EM map of DDB1:DCAF:Vpr State 1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Spodoptera frugiperda (fall armyworm)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)

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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: 7.8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k 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: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 7.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.07) / Number images used: 106747
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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