[English] 日本語
Yorodumi
- EMDB-5186: Structure of an apoptosome-procaspase-9 CARD complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-5186
TitleStructure of an apoptosome-procaspase-9 CARD complex
Map dataStructure of the human apoptosome with procaspase-9 CARD
Sample
  • Sample: human apoptosome with bound procaspase-9 CARD
  • Protein or peptide: Apaf-1
  • Protein or peptide: procaspase-9
  • Protein or peptide: cytochrome c
Keywordsapoptosome / Apaf-1 / procaspase-9 CARD / apoptosis
Function / homology
Function and homology information


: / Release of apoptotic factors from the mitochondria / Formation of apoptosome / Activation of caspases through apoptosome-mediated cleavage / Pyroptosis / Regulation of the apoptosome activity / Transcriptional activation of mitochondrial biogenesis / response to G1 DNA damage checkpoint signaling / regulation of apoptotic DNA fragmentation / Formation of apoptosome ...: / Release of apoptotic factors from the mitochondria / Formation of apoptosome / Activation of caspases through apoptosome-mediated cleavage / Pyroptosis / Regulation of the apoptosome activity / Transcriptional activation of mitochondrial biogenesis / response to G1 DNA damage checkpoint signaling / regulation of apoptotic DNA fragmentation / Formation of apoptosome / Detoxification of Reactive Oxygen Species / apoptosome / TP53 Regulates Metabolic Genes / Cytoprotection by HMOX1 / cysteine-type endopeptidase activator activity / Respiratory electron transport / Activation of caspases through apoptosome-mediated cleavage / Regulation of the apoptosome activity / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / mitochondrial electron transport, cytochrome c to oxygen / cysteine-type endopeptidase activator activity involved in apoptotic process / mitochondrial electron transport, ubiquinol to cytochrome c / TP53 Regulates Transcription of Caspase Activators and Caspases / Transcriptional Regulation by E2F6 / forebrain development / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / cellular response to transforming growth factor beta stimulus / heat shock protein binding / cardiac muscle cell apoptotic process / response to nutrient / intrinsic apoptotic signaling pathway / positive regulation of apoptotic signaling pathway / neural tube closure / kidney development / ADP binding / mitochondrial intermembrane space / nervous system development / neuron apoptotic process / secretory granule lumen / regulation of apoptotic process / ficolin-1-rich granule lumen / cell differentiation / response to hypoxia / electron transfer activity / positive regulation of apoptotic process / nucleotide binding / apoptotic process / heme binding / Neutrophil degranulation / protein-containing complex / extracellular exosome / extracellular region / ATP binding / metal ion binding / identical protein binding / nucleus / cytosol
Similarity search - Function
Apoptotic Protease-Activating Factor 1, CARD domain / : / Apoptotic protease-activating factor 1-like, winged-helix domain / Apoptotic protease-activating factor 1 / Apoptotic protease-activating factor 1 / APAF-1 helical domain / APAF-1 helical domain / Apoptotic protease-activating factors, helical domain / NB-ARC / NB-ARC domain ...Apoptotic Protease-Activating Factor 1, CARD domain / : / Apoptotic protease-activating factor 1-like, winged-helix domain / Apoptotic protease-activating factor 1 / Apoptotic protease-activating factor 1 / APAF-1 helical domain / APAF-1 helical domain / Apoptotic protease-activating factors, helical domain / NB-ARC / NB-ARC domain / Cytochrome c, class IA/ IB / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Cytochrome c / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Death-like domain superfamily / WD domain, G-beta repeat / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / Winged helix-like DNA-binding domain superfamily / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Apoptotic protease-activating factor 1 / Cytochrome c
Similarity search - Component
Biological speciesHomo sapiens (human) / Bos taurus (domestic cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 9.5 Å
AuthorsYuan S / Yu X / Topf M / Ludtke SJ / Wang X / Akey CW
CitationJournal: Structure / Year: 2010
Title: Structure of an apoptosome-procaspase-9 CARD complex.
Authors: Shujun Yuan / Xinchao Yu / Maya Topf / Steven J Ludtke / Xiaodong Wang / Christopher W Akey /
Abstract: Apaf-1 coassembles with cytochrome c to form the apoptosome, which then binds and activates procaspase-9 (pc-9). We removed pc-9 catalytic domains from the holoapoptosome by site-directed ...Apaf-1 coassembles with cytochrome c to form the apoptosome, which then binds and activates procaspase-9 (pc-9). We removed pc-9 catalytic domains from the holoapoptosome by site-directed thrombinolysis. A structure of the resulting apoptosome-pc-9 CARD complex was then determined at approximately 9.5 A resolution. In our model, the central hub is constructed like other AAA+ protein rings but also contains novel features. At higher radius, the regulatory region of each Apaf-1 is comprised of tandem seven and eight blade beta-propellers with cytochrome c docked between them. Remarkably, Apaf-1 CARDs are disordered in the ground state. During activation, each Apaf-1 CARD interacts with a pc-9 CARD and these heterodimers form a flexibly tethered "disk" that sits above the central hub. When taken together, the data reveal conformational changes during Apaf-1 assembly that allow pc-9 activation. The model also provides a plausible explanation for the effects of NOD mutations that have been mapped onto the central hub.
History
DepositionApr 13, 2010-
Header (metadata) releaseApr 29, 2010-
Map releaseMay 11, 2010-
UpdateApr 17, 2013-
Current statusApr 17, 2013Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.3
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1.3
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-3j2t
  • Surface level: 1.3
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-3j2t
  • Surface level: 1.3
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5186_1.jpg

Downloads & links

-
Map

FileDownload / File: emd_5186.map.gz / Format: CCP4 / Size: 29.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of the human apoptosome with procaspase-9 CARD
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.26 Å/pix.
x 200 pix.
= 452. Å		2.26 Å/pix.
x 200 pix.
= 452. Å		2.26 Å/pix.
x 200 pix.
= 452. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.26 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.3 / Movie #1: 1.3
Minimum - Maximum-3.31891465 - 5.20101023
Average (Standard dev.)0.03539509 (±0.24957854)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-100-100-100
Dimensions200200200
Spacing200200200
CellA=B=C: 452.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.262.262.26
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z452.000452.000452.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-34-26-72
NX/NY/NZ6953145
MAP C/R/S123
start NC/NR/NS-100-100-100
NC/NR/NS200200200
D min/max/mean-3.3195.2010.035

-
Supplemental data

-
Segmentation: This is a mask used to filter the final 3D volume

AnnotationThis is a mask used to filter the final 3D volume
Fileemd_5186_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : human apoptosome with bound procaspase-9 CARD

EntireName: human apoptosome with bound procaspase-9 CARD
Components
  • Sample: human apoptosome with bound procaspase-9 CARD
  • Protein or peptide: Apaf-1
  • Protein or peptide: procaspase-9
  • Protein or peptide: cytochrome c

-
Supramolecule #1000: human apoptosome with bound procaspase-9 CARD

SupramoleculeName: human apoptosome with bound procaspase-9 CARD / type: sample / ID: 1000
Details: Apoptosomes were assembled in low salt buffer, procaspase-9 with a thrombin site in the CARD-p20 linker was added, and then the complex was thrombinized to release pc-9 catalytic domains.
Oligomeric state: heptameric Apaf-1 in the apoptosome with 7 bound procaspase-9 CARDs
Number unique components: 3
Molecular weightTheoretical: 1.1 MDa

-
Macromolecule #1: Apaf-1

MacromoleculeName: Apaf-1 / type: protein_or_peptide / ID: 1 / Name.synonym: Apaf-1
Details: Seven Apaf-1 molecules were assembled with cytochrome c and dATP to form an apoptosome complex.
Number of copies: 7 / Oligomeric state: heptamer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Location in cell: cytosol
Molecular weightTheoretical: 135 KDa
Recombinant expressionOrganism: sf21 insect cells (unknown) / Recombinant plasmid: pFastBac1
SequenceGO: GO: 0008635 / InterPro: Apoptotic protease-activating factor 1

-
Macromolecule #2: procaspase-9

MacromoleculeName: procaspase-9 / type: protein_or_peptide / ID: 2 / Name.synonym: procaspase-9
Details: procaspase-9 binds on the human apoptosome through CARD-CARD interactions. Procaspase-9 was added to the apoptosome in slight excess and then thrombinized to remove the catalytic domains.
Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Location in cell: cytosol
Molecular weightTheoretical: 10 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pET21b

-
Macromolecule #3: cytochrome c

MacromoleculeName: cytochrome c / type: protein_or_peptide / ID: 3 / Name.synonym: cytochrome c / Details: cytochrome c is the assembly activator for Apaf-1 / Number of copies: 7 / Oligomeric state: monomer / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Bos taurus (domestic cattle) / synonym: cow / Organelle: mitochrondria
Molecular weightTheoretical: 10 KDa

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration3 mg/mL
BufferpH: 7.5
Details: 20mM HEPES, 10mM KCl, 1.5mM MgCl2, 1mM EDTA, 1mM EGTA, 1mM DTT
GridDetails: Quantifoil R1.2/1.3 holey grids
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 77 K / Instrument: FEI VITROBOT MARK III / Details: Vitrification instrument: Vitrobot Mark 3 (FEI) / Method: Blot for 2-3 seconds before plunging at 20C

-
Electron microscopy

MicroscopeFEI TECNAI F20
TemperatureAverage: 96 K
Alignment procedureLegacy - Astigmatism: objective lens astigmatism was corrected at 200,000 times magnification
DateAug 1, 2008
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 400 / Average electron dose: 25 e/Å2 / Od range: 1
Electron beamAcceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 62000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 62000
Sample stageSpecimen holder: Side entry liquid nitrogen-cooled cryo specimen holder.
Specimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

-
Image processing

Detailsparticles were selected with boxer
CTF correctionDetails: Each image
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 9.5 Å / Resolution method: OTHER / Software - Name: EMAN
Details: Final map contains 34000 particles. Setsf filtration was applied to the final map to boost amplitude at high resolution range and in the last cycles of refinement.
Number images used: 42000
Final two d classificationNumber classes: 592

-
Atomic model buiding 1

Initial modelPDB ID:

1z6t


Chain - Chain ID: A
SoftwareName: chimera
DetailsPDBEntryID_givenInChain. Protocol: rigid body for each domain. After chimera fitting, Flex-EM was used to improve fitting and minimize collisions. The beta propellers were modeled using the map as a restraint, sequence alignments and the crystal structure of actin interacting protein 1.
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: cross correlation
Output model

PDB-3j2t:
An improved model of the human apoptosome

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
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.
  • 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

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more