[English] 日本語
Yorodumi
- PDB-3j2t: An improved model of the human apoptosome -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3j2t
TitleAn improved model of the human apoptosome
Components
  • Apoptotic protease-activating factor 1
  • Cytochrome c
KeywordsAPOPTOSIS / Apoptosis protease activating factor-1 / Apaf-1 / cytochrome c
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 / Detoxification of Reactive Oxygen Species ...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 / APAF-1 helical domain / APAF-1 helical domain / Apoptotic protease-activating factors, helical domain / NB-ARC / NB-ARC domain / Cytochrome c, class IA/ IB ...Apoptotic Protease-Activating Factor 1, CARD domain / : / Apoptotic protease-activating factor 1-like, winged-helix domain / 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
ADENOSINE-5'-TRIPHOSPHATE / PROTOPORPHYRIN IX CONTAINING FE / Apoptotic protease-activating factor 1 / Cytochrome c
Similarity search - Component
Biological speciesHomo sapiens (human)
Bos taurus (domestic cattle)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 9.5 Å
AuthorsYuan, S. / Topf, M. / Akey, C.W.
Citation
Journal: Biochemistry / Year: 2013
Title: Changes in Apaf-1 conformation that drive apoptosome assembly.
Authors: Shujun Yuan / Maya Topf / Thomas F Reubold / Susanne Eschenburg / Christopher W Akey /
Abstract: Apoptosome assembly is highly regulated in the intrinsic cell death pathway. To better understand this step, we created an improved model of the human apoptosome using a crystal structure of full ...Apoptosome assembly is highly regulated in the intrinsic cell death pathway. To better understand this step, we created an improved model of the human apoptosome using a crystal structure of full length Apaf-1 and a single particle, electron density map at ~9.5 Å resolution. The apoptosome model includes N-terminal domains of Apaf-1, cognate β-propellers, and cytochrome c. A direct comparison of Apaf-1 in the apoptosome and as a monomer reveals conformational changes that occur during the first two steps of assembly. This includes an induced-fit mechanism for cytochrome c binding to regulatory β-propellers, which is dependent on shape and charge complementarity, and a large rotation of the nucleotide binding module during nucleotide exchange. These linked conformational changes create an extended Apaf-1 monomer and drive apoptosome assembly. Moreover, the N-terminal CARD in the inactive Apaf-1 monomer is not shielded from other proteins by β-propellers. Hence, the Apaf-1 CARD may be free to interact with a procaspase-9 CARD either before or during apoptosome assembly. Irrespective of the timing, the end product of assembly is a holo-apoptosome with an acentric CARD-CARD disk and tethered pc-9 catalytic domains. Subsequent activation of pc-9 leads to a proteolytic cascade and cell death.
#1: Journal: 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
DepositionDec 23, 2012Deposition site: RCSB / Processing site: RCSB
SupersessionApr 10, 2013ID: 3IZA
Revision 1.0Apr 10, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2013Group: Database references
Revision 1.2Jul 18, 2018Group: Data collection / Category: em_software / Item: _em_software.image_processing_id
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-5186
  • Imaged by UCSF Chimera
  • Download
  • Superimposition on EM map
  • EMDB-5186
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Apoptotic protease-activating factor 1
B: Apoptotic protease-activating factor 1
C: Apoptotic protease-activating factor 1
D: Apoptotic protease-activating factor 1
E: Apoptotic protease-activating factor 1
F: Apoptotic protease-activating factor 1
G: Apoptotic protease-activating factor 1
H: Cytochrome c
I: Cytochrome c
J: Cytochrome c
K: Cytochrome c
L: Cytochrome c
M: Cytochrome c
N: Cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,097,70428
Polymers1,089,83814
Non-polymers7,86614
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

#1: Protein
Apoptotic protease-activating factor 1 / APAF-1


Mass: 144095.812 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Apaf-1, APAF1, KIAA0413 / Plasmid: pFastBac1 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): sf21 / References: UniProt: O14727
#2: Protein
Cytochrome c


Mass: 11595.392 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P62894
#3: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C34H32FeN4O4
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

Component
IDNameTypeDetailsParent-ID
1Human Apaf-1 apoptosome with stably bound cytochrome c and procaspase-9 CARDs.COMPLEXRecombinant procaspase-9 was added to form pc-9 apoptosomes and thrombin was added to cleave an engineered site in the CARD-p20 linker of pc-9. This released catalytic domains of pc-9 and left pc-9 CARDs bound to flexibly attached Apaf-1 CARDs which together form a flexibly attached disk that sits on top of the Apaf-1 platform. The CARD-CARD disk has not been modeled due to flexibility.0
2Apaf-17 Apaf-1 and 7 cytochrome c molecules were co-assembled to form a heptameric apoptosome1
Buffer solutionName: low salt HEPES buffer / pH: 7.5
Details: 20mM HEPES, 10mM KCl, 1.5mM MgCl2, 1mM EDTA, 1mM EGTA, 1mM DTT
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Quantifoil R1.2/1.3 holey grid
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Temp: 77 K / Humidity: 100 %
Details: Blot for 2 seconds before plunging (FEI VITROBOT MARK III)
Method: Blot for 2 seconds before plunging

-
Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20 / Date: Aug 1, 2008
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 120 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 62000 X / Calibrated magnification: 62000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1500 nm / Cs: 2 mm
Specimen holderSpecimen holder model: GATAN LIQUID NITROGEN
Specimen holder type: Side entry liquid nitrogen-cooled cryo specimen holder
Temperature: 96 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 25 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNum. digital images: 400
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

-
Processing

EM software
IDNameCategory
1Rosettamodel fitting
2Situsmodel fitting
3UCSF Chimeramodel fitting
4EMAN3D reconstruction
CTF correctionDetails: CTF correction was done on each particle image based on summed power spectra from each micrograph.
SymmetryPoint symmetry: C7 (7 fold cyclic)
3D reconstructionMethod: Projection Matching / Resolution: 9.5 Å / Num. of particles: 34000 / Nominal pixel size: 2.26 Å / Actual pixel size: 2.26 Å / Magnification calibration: TMV images
Details: EMAN was used for reconstruction using C7 symmetry.
Symmetry type: POINT
Atomic model building
IDProtocolSpaceTarget criteriaDetails
1FLEXIBLE FITREALCross-correlation coefficientMETHOD--flexible fitting REFINEMENT PROTOCOL--Rigid body docking followed by flexible fitting DETAILS--Modeller was used to create a full length human Apaf-1. Initial fit was done using Chimera rigid body fitting. Rosetta was used for flexible fitting.
2RIGID BODY FITREALCross-correlation coefficientMETHOD--rigid body fitting REFINEMENT PROTOCOL--rigid body DETAILS--Cytochrome c was fitted into its local density using Situs.
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
11Z6T

1z6t

11Z6T1PDBexperimental model
23SFZ

3sfz

13SFZ2PDBexperimental model
32B4Z

2b4z

22B4Z3PDBexperimental model
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms69671 0 518 0 70189

+
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