PDBe 5wve

Electron Microscopy
4.4Å resolution

Apaf-1-Caspase-9 holoenzyme

Released:
Source organisms:
Primary publication:
Mechanistic insights into caspase-9 activation by the structure of the apoptosome holoenzyme.
Proc. Natl. Acad. Sci. U.S.A. 114 1542-1547 (2017)
PMID: 28143931
Related structures: EMD-6690

Function and Biology Details

Reaction catalysed:
Strict requirement for an Asp residue at position P1 and with a marked preference for His at position P2. It has a preferred cleavage sequence of Leu-Gly-His-Asp-|-Xaa
Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero 25-mer (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
Apoptotic protease-activating factor 1 Chains: A, C, E, G, I, K, M
Molecule details ›
Chains: A, C, E, G, I, K, M
Length: 1248 amino acids
Theoretical weight: 142.02 KDa
Source organism: Homo sapiens
Expression system: Insect cell expression vector pTIE1
UniProt:
  • Canonical: NEW O14727 (Residues: 1-1248; Coverage: 100%)
Gene names: APAF1, KIAA0413
Sequence domains:
Cytochrome c Chains: B, D, F, H, J, L, N
Molecule details ›
Chains: B, D, F, H, J, L, N
Length: 105 amino acids
Theoretical weight: 11.86 KDa
Source organism: Equus caballus
Expression system: Bacteria
UniProt:
  • Canonical: NEW P00004 (Residues: 1-105; Coverage: 100%)
Gene names: CYC, CYCS
Sequence domains: Cytochrome c
Apoptotic protease-activating factor 1 Chains: O, P, Q, R, W, X
Molecule details ›
Chains: O, P, Q, R, W, X
Length: 102 amino acids
Theoretical weight: 11.58 KDa
Source organism: Homo sapiens
Expression system: Insect cell expression vector pTIE1
UniProt:
  • Canonical: NEW O14727 (Residues: 1-102; Coverage: 8%)
Gene names: APAF1, KIAA0413
Sequence domains: Caspase recruitment domain
Caspase-9 subunit p35 Chains: S, T, U, V, Y
Molecule details ›
Chains: S, T, U, V, Y
Length: 100 amino acids
Theoretical weight: 11.7 KDa
Source organism: Homo sapiens
Expression system: Bacteria
UniProt: Gene names: CASP9, MCH6
Sequence domains: Caspase recruitment domain

Ligands and Environments

3 bound ligands:

No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 4.4Å
Relevant EMDB volumes: EMD-6690
Expression systems:
  • Insect cell expression vector pTIE1
  • Bacteria