3JBT | pdb_00003jbt

Atomic structure of the Apaf-1 apoptosome

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history. 

Literature

Atomic structure of the apoptosome: mechanism of cytochrome c- and dATP-mediated activation of Apaf-1

Zhou, M., Li, Y., Hu, Q., Bai, X.C., Huang, W., Yan, C., Scheres, S.H.W., Shi, Y.

(2015) Genes Dev 29: 2349-2361

  • DOI: https://doi.org/10.1101/gad.272278.115
  • Primary Citation Related Structures: 
    3JBT

  • PubMed Abstract: 

    The apoptotic protease-activating factor 1 (Apaf-1) controls the onset of many known forms of intrinsic apoptosis in mammals. Apaf-1 exists in normal cells as an autoinhibited monomer. Upon binding to cytochrome c and dATP, Apaf-1 oligomerizes into a heptameric complex known as the apoptosome, which recruits and activates cell-killing caspases. Here we present an atomic structure of an intact mammalian apoptosome at 3.8 Å resolution, determined by single-particle, cryo-electron microscopy (cryo-EM). Structural analysis, together with structure-guided biochemical characterization, uncovered how cytochrome c releases the autoinhibition of Apaf-1 through specific interactions with the WD40 repeats. Structural comparison with autoinhibited Apaf-1 revealed how dATP binding triggers a set of conformational changes that results in the formation of the apoptosome. Together, these results constitute the molecular mechanism of cytochrome c- and dATP-mediated activation of Apaf-1.

    • Organizational Affiliation: 
    • Ministry of Education Protein Science Laboratory, Center for Structural Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, School of Medicine, Tsinghua University, Beijing 100084, China;

Macromolecule Content 

  • Total Structure Weight: 1,096.45 kDa 
  • Atom Count: 70,252 
  • Modeled Residue Count: 8,736 
  • Deposited Residue Count: 9,555 
  • Unique protein chains: 2

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Apoptotic protease-activating factor 1
A, C, E, G, I
A, C, E, G, I, K, M
1,260Homo sapiensMutation(s): 0 
Gene Names: APAF1, KIAA0413
UniProt & NIH Common Fund Data Resources
Find proteins for O14727 (Homo sapiens)
Explore O14727 
Go to UniProtKB:  O14727
PHAROS:  O14727
GTEx:  ENSG00000120868 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO14727
Sequence Annotations
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Reference Sequence
Find similar proteins by:
|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c
B, D, F, H, J
B, D, F, H, J, L, N
105Equus caballusMutation(s): 0 
UniProt
Find proteins for P00004 (Equus caballus)
Explore P00004 
Go to UniProtKB:  P00004
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00004
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM

Query on HEM


Download:Ideal Coordinates CCD File
CA [auth J]
FA [auth L]
IA [auth N]
Q [auth B]
T [auth D]
CA [auth J],
FA [auth L],
IA [auth N],
Q [auth B],
T [auth D],
W [auth F],
Z [auth H]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
DTP

Query on DTP


Download:Ideal Coordinates CCD File
AA [auth I]
DA [auth K]
GA [auth M]
O [auth A]
R [auth C]
AA [auth I],
DA [auth K],
GA [auth M],
O [auth A],
R [auth C],
U [auth E],
X [auth G]
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
C10 H16 N5 O12 P3
SUYVUBYJARFZHO-RRKCRQDMSA-N
MG

Query on MG


Download:Ideal Coordinates CCD File
BA [auth I]
EA [auth K]
HA [auth M]
P [auth A]
S [auth C]
BA [auth I],
EA [auth K],
HA [auth M],
P [auth A],
S [auth C],
V [auth E],
Y [auth G]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-11-18
    Type: Initial release
  • Version 1.1: 2017-01-18
    Changes: Database references
  • Version 1.2: 2019-10-16
    Changes: Data collection, Database references, Other
  • Version 1.3: 2019-12-18
    Changes: Data collection, Database references, Other
  • Version 1.4: 2024-11-20
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary