[English] 日本語
- EMDB-1931: Map of the apoptosome-procaspase-9 complex -

Open data

ID or keywords:


no data

Basic information

Database: EMDB / ID: 1931
TitleMap of the apoptosome-procaspase-9 complex
Keywordsapoptosome / Apaf-1 / procaspase-9 activation
SampleHuman apoptosome-procaspase-9 complex
SourceHomo sapiens / human /
Bos taurus / mammal / Cow / Cattle /
Map dataMap of the apoptosome-procaspase-9 complex
Methodsingle particle reconstruction, at 16.9 Å resolution
AuthorsYuan S / Ludtke SJ / Akey CW
CitationStructure, 2011, 19, 1084-1096

Structure, 2011, 19, 1084-1096 Yorodumi Papers
The holo-apoptosome: activation of procaspase-9 and interactions with caspase-3.
Shujun Yuan / Xinchao Yu / John M Asara / John E Heuser / Steven J Ludtke / Christopher W Akey

DateDeposition: Jul 12, 2011 / Header (metadata) release: Mar 15, 2012 / Map release: Mar 15, 2012 / Last update: Mar 15, 2012

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 0.8
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.8
  • Imaged by UCSF CHIMERA
  • Download
3D viewer
Supplemental images

Downloads & links


Fileemd_1931.map.gz (map file in CCP4 format, 27649 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
192 pix
2.9 Å/pix.
= 556.8 Å
192 pix
2.9 Å/pix.
= 556.8 Å
192 pix
2.9 Å/pix.
= 556.8 Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 2.9 Å
Contour Level:0.8 (by author), 0.8 (movie #1):
Minimum - Maximum-0.67261672 - 2.2649889
Average (Standard dev.)0.01628205 (0.14226763)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA=B=C: 556.80005 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.92.92.9
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z556.800556.800556.800
start NX/NY/NZ-56-56-55
MAP C/R/S123
start NC/NR/NS000
D min/max/mean-0.6732.2650.016

Supplemental data

Sample components

Entire Human apoptosome-procaspase-9 complex

EntireName: Human apoptosome-procaspase-9 complex
Details: A slight excess of procaspase-9 was added to ensure saturation of binding to sites on the apoptosome.
Number of components: 3
Oligomeric State: 5-7 procaspase-9 molecules bound to the human apoptosome comprised of 7 Apaf-1 subunits
MassTheoretical: 1.2 MDa

Component #1: protein, Apaf-1

ProteinName: Apaf-1 / a.k.a: Apaf-1 / Oligomeric Details: Heptamer
Details: Apaf-1, cytochrome c and procaspase-9 were co-assembled in the presence of dATP to form the apoptosome-procaspase-9 complex
Number of Copies: 7 / Recombinant expression: Yes
MassTheoretical: 130 kDa
SourceSpecies: Homo sapiens / human /
Source (engineered)Expression System: Spodoptera frugiperda / arthropod / Fall armyworm
Vector: pFastBac1
Source (natural)Location in cell: Cytosol
External referencesInterPro: InterPro: 017251

Component #2: protein, Procaspase-9

ProteinName: Procaspase-9 / a.k.a: Procaspase-9 / Oligomeric Details: Monomer / Recombinant expression: Yes
MassTheoretical: 50 kDa
SourceSpecies: Homo sapiens / human /
Source (engineered)Expression System: Escherichia coli / bacteria / / / Vector: pET21
Source (natural)Location in cell: Cytosol

Component #3: protein, Cytochrome c

ProteinName: Cytochrome c / a.k.a: Cytochrome c / Oligomeric Details: Monomer / Recombinant expression: No / Number of Copies: 7
MassTheoretical: 10 kDa
SourceSpecies: Bos taurus / mammal / Cow / Cattle /
Source (natural)Location in cell: Mitochondria / Organ or tissue: heart

Experimental details

Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 3 mg/ml
Buffer solution: 20 mM HEPES, 10 mM KCl, 1.5 mM MgCl2, 1 mM EDTA, 1 mM EGTA, 1 mM DTT
pH: 7.5
Support filmQuantifoil holey grids
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Temperature: 77 K / Humidity: 100 % / Method: Blot for 2-3 seconds before plunging at 20C / Details: Vitrification instrument: Vitrobot Mark 3 (FEI)

Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F20 / Details: 4k x 4k ccd used
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 120 kV / Electron dose: 20 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 29000 X (nominal), 29000 X (calibrated)
Astigmatism: objective lens astigmatism was corrected at 200,000 times magnification
Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1800 - 3500 nm
Specimen HolderHolder: Side entry liquid nitrogen-cooled cryo specimen holder
Model: GATAN LIQUID NITROGEN / Temperature: 96 K
CameraDetector: GENERIC TVIPS

Image acquisition

Image acquisitionNumber of digital images: 447

Image processing

ProcessingMethod: single particle reconstruction / Number of class averages: 1000 / Number of projections: 20000
Details: Apaf-1 was co-assembled with bovine cytochrome c and pc-9
Applied symmetry: C1 (asymmetric)
3D reconstructionAlgorithm: Projection matching / Software: EMAN2 / CTF correction: Each image
Details: 3D volume was calculated without imposing any symmetry (c1)
Resolution: 16.9 Å / Resolution method: FSC 0.5

Atomic model buiding

Modeling #1Software: chimera / Refinement protocol: rigid body / Target criteria: cross correlation / Refinement space: REAL / Details: Protocol: rigid body
Input PDB model: 3IZA
Modeling #2Software: chimera / Refinement protocol: rigid body / Refinement space: REAL
Details: Protocol: rigid body. final fit was done manually taking into account the orientation of the p20-p10 loop.
Input PDB model: 1JXQ
Chain ID: 1JXQ_A

About Yorodumi


Oct 4, 2017. Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

  • Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
  • Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
  • Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.

External links: The 2017 Nobel Prize in Chemistry - Press Release

Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

Read more


Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • All the functionalities will be ported from the levgacy version.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Changes in new EM Navigator and Yorodumi

Read more