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- EMDB-6691: Apaf-1-Caspase-9 holoenzyme -

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Basic information

Entry
Database: EMDB / ID: 6691
TitleApaf-1-Caspase-9 holoenzyme
SampleApaf-1 apoptosome
SourceHomo sapiens / human
Map dataNone
Methodsingle particle reconstruction, at 4.4 Å resolution
AuthorsLi Y / Zhou M / Hu Q / Bai X / Huang W / Scheres SHW / Shi Y
CitationProc. Natl. Acad. Sci. U.S.A., 2017, 114, 1542-1547

Proc. Natl. Acad. Sci. U.S.A., 2017, 114, 1542-1547 StrPapers
Mechanistic insights into caspase-9 activation by the structure of the apoptosome holoenzyme.
Yini Li / Mengying Zhou / Qi Hu / Xiao-Chen Bai / Weiyun Huang / Sjors H W Scheres / Yigong Shi

DateDeposition: Dec 24, 2016 / Header (metadata) release: Jan 18, 2017 / Map release: Mar 1, 2017 / Last update: Dec 24, 2016

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0563
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0563
  • Imaged by UCSF CHIMERA
  • Download
3D viewer


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Supplemental images

Downloads & links

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Map

Fileemd_6691.map.gz (map file in CCP4 format, 131073 KB)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
320 pix
1.34 Å/pix.
= 428.8 Å
320 pix
1.34 Å/pix.
= 428.8 Å
320 pix
1.34 Å/pix.
= 428.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.34 Å
Density
Contour Level:0.0563 (by author), 0.0563 (movie #1):
Minimum - Maximum-0.21274799 - 0.48513398
Average (Standard dev.)0.0012616193 (0.01155583)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions320320320
Origin000
Limit319319319
Spacing320320320
CellA=B=C: 428.80002 Å
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/pix X/Y/Z1.341.341.34
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z428.800428.800428.800
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.2130.4850.001

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Supplemental data

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Sample components

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Entire Apaf-1 apoptosome

EntireName: Apaf-1 apoptosome / Number of components: 1

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Component #1: protein, Apaf-1 apoptosome

ProteinName: Apaf-1 apoptosome / Recombinant expression: No
SourceSpecies: Homo sapiens / human
Source (engineered)Expression System: Insect cell expression vector ptie1 / Vector: pFasBac

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
ImagingMicroscope: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 32 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON II (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 240130
3D reconstructionResolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF

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