3YGS: Apaf-1 card

Apaf-1 card in complex with prodomain of procaspase-9. Determined by X-ray diffraction at 2.5 Å resolution. Released 19 Apr 2000.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Homo sapiens
Chains: 2
Atoms: 1,726
Mol. weight: 22.24 kDa
Released: 19 Apr 2000

Explore 3YGS in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3YGS contains 14 α-helices and 0 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain C: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	3-17	15
α-helix	22-32	11
α-helix	37-44	8
α-helix	49-61	13
α-helix	65-77	13
α-helix	81-87	7
α-helix	88-90	3

Chain P: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	4-12	9
α-helix	14-20	7
α-helix	27-32	6
α-helix	38-45	8
α-helix	52-63	12
α-helix	70-79	10
α-helix	84-95	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Apoptotic protease activating factor 1	C	protein	95	Homo sapiens	O14727 (AlphaFold model)
Procaspase 9	P	protein	97	Homo sapiens	P55211 (AlphaFold model)

Sequence of entity 1 (C), FASTA

>3YGS_1 APOPTOTIC PROTEASE ACTIVATING FACTOR 1 (chains C)
MDAKARNCLLQHREALEKDIKTSYIMDHMISDGFLTISEEEKVRNEPTQQQRAAMLIKMI
LKKDNDSYVSFYNALLHEGYKDLAALLHDGIPVVS

Sequence of entity 2 (P), FASTA

>3YGS_2 PROCASPASE 9 (chains P)
SMDEADRRLLRRCRLRLVEELQVDQLWDVLLSRELFRPHMIEDIQRAGSGSRRDQARQLI
IDLETRGSQALPLFISCLEDTGQDMLASFLRTNRQAG

Primary citation

Structural basis of procaspase-9 recruitment by the apoptotic protease-activating factor 1. Qin, H., Srinivasula, S.M., Wu, G. et al. Nature (1999) 399:549-557. DOI 10.1038/21124 · PubMed

Other PDB entries of the same protein (UniProt O14727 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1CY5 1.3 Å, Crystal structure of the apaf-1 card
2P1H 1.59 Å, Rapid Folding and Unfolding of Apaf-1 CARD
2YGS 1.6 Å, Card domain from apaf-1
4RHW 2.1 Å, Crystal structure of Apaf-1 CARD and caspase-9 CARD complex
1Z6T 2.21 Å, Structure of the apoptotic protease-activating factor 1 bound to ADP
8XQK 2.85 Å, The Crystal Structure of Apaf from Biortus.
5WVC 2.99 Å, Structure of the CARD-CARD disk
3JBT 3.8 Å, Atomic structure of the Apaf-1 apoptosome
5JUY 4.1 Å, Active human apoptosome with procaspase-9
5WVE 4.4 Å, Apaf-1-Caspase-9 holoenzyme
3J2T 9.5 Å, An improved model of the human apoptosome
1C15 Solution structure of apaf-1 card

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