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- EMDB-9669: Cryo-EM Structure of Human SRCAP full complex -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-9669
TitleCryo-EM Structure of Human SRCAP full complex
Map datadull complex. 8.5 Angstrom.
Sample
  • Complex: SRCAP complex
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.5 Å
AuthorsFeng Y / Tian Y / Wu Z / Xu Y
CitationJournal: Cell Res / Year: 2018
Title: Cryo-EM structure of human SRCAP complex.
Authors: Yangyang Feng / Yuan Tian / Zihan Wu / Yanhui Xu /
History
DepositionSep 25, 2018-
Header (metadata) releaseJul 24, 2019-
Map releaseJul 24, 2019-
UpdateJul 24, 2019-
Current statusJul 24, 2019Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0105
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0105
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9669.png

Downloads & links

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Map

FileDownload / File: emd_9669.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationdull complex. 8.5 Angstrom.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 320 pix.
= 432. Å		1.35 Å/pix.
x 320 pix.
= 432. Å		1.35 Å/pix.
x 320 pix.
= 432. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0105 / Movie #1: 0.0105
Minimum - Maximum-0.015253694 - 0.04328775
Average (Standard dev.)0.00024046072 (±0.0019022503)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 432.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z432.000432.000432.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.0150.0430.000

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Supplemental data

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Sample components

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Entire : SRCAP complex

EntireName: SRCAP complex
Components
  • Complex: SRCAP complex

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Supramolecule #1: SRCAP complex

SupramoleculeName: SRCAP complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Mammalia (mammals)

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 1.5625 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

Final reconstructionResolution.type: BY AUTHOR / Resolution: 8.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 15248
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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