5WVE: Apaf-1-Caspase-9 holoenzyme

Apaf-1-Caspase-9 holoenzyme. Determined by electron microscopy at 4.4 Å resolution. Released 8 Feb 2017.

Method: Electron microscopy
Resolution: 4.4 Å
Organisms: Homo sapiens, Equus caballus
Chains: 25
Atoms: 78,605
Mol. weight: 1213.03 kDa
Ligands: HEM, MG, DTP
Released: 8 Feb 2017

Explore 5WVE in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5WVE contains 358 α-helices and 539 β-strands across 25 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.

Chains A, C, G, K and M: 34 helices, 75 β-strands

Element	Residues	Length	Sheet
α-helix	108-117	10
α-helix	119-123	5
α-helix	130-142	13
β-strand	149-153	5	1
α-helix	160-169	10
α-helix	171-177	7
β-strand	182-188	7	1
α-helix	192-206	15
α-helix	220-229	10
α-helix	230-234	5
β-strand	239-244	6	1
α-helix	248-254	7
β-strand	260-264	5	1
β-strand	277-281	5	1
α-helix	288-299	12
α-helix	308-317	10
α-helix	321-333	13
α-helix	338-347	10
α-helix	364-373	10
α-helix	377-385	9
β-strand	395-396	2	2
α-helix	397-404	8
α-helix	408-420	13
β-strand	425	1	3
β-strand	428	1	4
β-strand	433	1	4
β-strand	434-435	2	2
β-strand	436	1	3
α-helix	439-466	28
α-helix	480-494	15
α-helix	497-503	7
α-helix	507-517	11
α-helix	521-532	12
α-helix	535-549	15
α-helix	551-554	4
α-helix	563-566	4
α-helix	574-590	17
α-helix	594-596	3
β-strand	597	1	5
α-helix	600-602	3
β-strand	609-611	3	6
α-helix	617-618	2
β-strand	621-623	3	7
β-strand	630-632	3	7
β-strand	640-643	4	7
β-strand	648-652	5	7
β-strand	660-665	6	8
β-strand	671-676	6	8
β-strand	681-685	5	8
β-strand	691-695	5	8
β-strand	702-707	6	9
β-strand	715-720	6	9
β-strand	725-729	5	9
β-strand	735-739	5	9
β-strand	746-749	4	10
β-strand	757-762	6	10
β-strand	768-771	4	10
β-strand	776-779	4	10
β-strand	804-806	3	11
β-strand	813-817	5	11
β-strand	820-825	6	11
β-strand	830-833	4	11
β-strand	836	1	11
α-helix	837	1
β-strand	848	1	12
α-helix	851-853	3
β-strand	854-858	5	12
β-strand	864-868	5	12
β-strand	873-876	4	12
β-strand	885-890	6	6
β-strand	896-901	6	6
β-strand	906-910	5	6
α-helix	911-915	5
β-strand	928-930	3	13
β-strand	935-937	3	13
β-strand	946-947	2	14
β-strand	949-950	2	13
β-strand	958-959	2	14
β-strand	967-969	3	15
α-helix	970	1
β-strand	975	1	16
β-strand	976-978	3	15
β-strand	985-986	2	15
β-strand	989	1	16
β-strand	998-999	2	15
β-strand	1009-1011	3	17
β-strand	1018-1020	3	17
β-strand	1027-1031	5	17
β-strand	1036-1040	5	17
β-strand	1049-1052	4	18
β-strand	1057-1061	5	18
β-strand	1067-1071	5	18
β-strand	1079-1081	3	18
β-strand	1090-1093	4	19
β-strand	1101-1104	4	19
β-strand	1109-1112	4	19
β-strand	1121-1123	3	19
β-strand	1132-1135	4	20
β-strand	1142-1145	4	20
β-strand	1151	1	20
α-helix	1162-1164	3
β-strand	1182-1185	4	21
β-strand	1191-1195	5	21
β-strand	1199-1203	5	21
β-strand	1220	1	22
β-strand	1233-1235	3	23
β-strand	1236	1	22
β-strand	1241-1243	3	23
β-strand	1244	1	5

Chains B, D, F, H, J, L and N: 6 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	3-13	11
α-helix	24-26	3
β-strand	39	1	24
α-helix	50-54	5
β-strand	58	1	24
α-helix	61-69	9
α-helix	71-74	4
α-helix	88-101	14

Chains E and I: 34 helices, 75 β-strands

Element	Residues	Length	Sheet
α-helix	108-117	10
α-helix	119-123	5
α-helix	130-142	13
β-strand	149-153	5	49
α-helix	160-169	10
α-helix	171-177	7
β-strand	182-188	7	49
α-helix	192-206	15
α-helix	220-229	10
α-helix	230-234	5
β-strand	239-244	6	49
α-helix	248-254	7
β-strand	260-264	5	49
β-strand	277-281	5	49
α-helix	288-299	12
α-helix	310-317	8
α-helix	321-333	13
α-helix	338-347	10
α-helix	364-373	10
α-helix	377-385	9
β-strand	395-396	2	50
α-helix	397-404	8
α-helix	408-420	13
β-strand	425	1	51
β-strand	428	1	52
β-strand	433	1	52
β-strand	434-435	2	50
β-strand	436	1	51
α-helix	439-466	28
α-helix	480-494	15
α-helix	497-503	7
α-helix	507-517	11
α-helix	521-532	12
α-helix	535-549	15
α-helix	551-554	4
α-helix	563-566	4
α-helix	574-590	17
α-helix	594-596	3
β-strand	597	1	53
α-helix	600-602	3
β-strand	609-611	3	54
α-helix	617-618	2
β-strand	621-623	3	55
β-strand	630-632	3	55
β-strand	640-643	4	55
β-strand	648-652	5	55
β-strand	660-665	6	56
β-strand	671-676	6	56
β-strand	681-685	5	56
β-strand	691-695	5	56
β-strand	702-707	6	57
β-strand	715-720	6	57
β-strand	725-729	5	57
β-strand	735-739	5	57
β-strand	746-749	4	58
β-strand	757-762	6	58
β-strand	768-771	4	58
β-strand	776-779	4	58
β-strand	804-806	3	59
β-strand	813-817	5	59
β-strand	820-825	6	59
β-strand	830-833	4	59
β-strand	836	1	59
α-helix	837	1
β-strand	848	1	60
α-helix	851-853	3
β-strand	854-858	5	60
β-strand	864-868	5	60
β-strand	873-876	4	60
β-strand	885-890	6	54
β-strand	896-901	6	54
β-strand	906-910	5	54
α-helix	911-915	5
β-strand	928-930	3	61
β-strand	935-937	3	61
β-strand	946-947	2	62
β-strand	949-950	2	61
β-strand	958-959	2	62
β-strand	967-969	3	63
α-helix	970	1
β-strand	975	1	64
β-strand	976-978	3	63
β-strand	985-986	2	63
β-strand	989	1	64
β-strand	998-999	2	63
β-strand	1009-1011	3	65
β-strand	1018-1020	3	65
β-strand	1027-1031	5	65
β-strand	1036-1040	5	65
β-strand	1049-1052	4	66
β-strand	1057-1061	5	66
β-strand	1067-1071	5	66
β-strand	1079-1081	3	66
β-strand	1090-1093	4	67
β-strand	1101-1104	4	67
β-strand	1109-1112	4	67
β-strand	1121-1123	3	67
β-strand	1132-1135	4	68
β-strand	1142-1145	4	68
β-strand	1151	1	68
α-helix	1162-1164	3
β-strand	1182-1185	4	69
β-strand	1191-1195	5	69
β-strand	1199-1203	5	69
β-strand	1220	1	70
β-strand	1233-1235	3	71
β-strand	1236	1	70
β-strand	1241-1243	3	71
β-strand	1244	1	53

Chain O: 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	49-60	12
α-helix	65-77	13
α-helix	81-87	7
α-helix	88-90	3

Chains P, Q and R: 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

Chains S, T and V: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	3-11	9
α-helix	13-19	7
α-helix	26-31	6
α-helix	37-44	8
α-helix	51-62	12
α-helix	69-78	10
α-helix	83-94	12

Chain U: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	3-11	9
α-helix	13-17	5
α-helix	26-31	6
α-helix	37-44	8
α-helix	51-62	12
α-helix	69-78	10
α-helix	83-94	12

Chain W: 9 helices, 0 β-strands

Element	Residues	Length
α-helix	3-11	9
α-helix	13-19	7
α-helix	22-24	3
α-helix	26-31	6
α-helix	37-44	8
α-helix	49-60	12
α-helix	65-77	13
α-helix	81-88	8
α-helix	91-93	3

2 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Apoptotic protease-activating factor 1	A, C, E, G, I, K, M	protein	1248	Homo sapiens	O14727 (AlphaFold model)
Cytochrome c	B, D, F, H, J, L, N	protein	105	Equus caballus	P00004 (AlphaFold model)
Apoptotic protease-activating factor 1	O, P, Q, R, W, X	protein	102	Homo sapiens	O14727 (AlphaFold model)
Caspase	S, T, U, V, Y	protein	100	Homo sapiens	P55211 (AlphaFold model)

Sequence of entity 1 (A, C, E, G, I, K, M), FASTA

>5WVE_1 Apoptotic protease-activating factor 1 (chains A, C, E, G, I, K, M)
MDAKARNCLLQHREALEKDIKTSYIMDHMISDGFLTISEEEKVRNEPTQQQRAAMLIKMI
LKKDNDSYVSFYNALLHEGYKDLAALLHDGIPVVSSSSGKDSVSGITSYVRTVLCEGGVP
QRPVVFVTRKKLVNAIQQKLSKLKGEPGWVTIHGMAGCGKSVLAAEAVRDHSLLEGCFPG
GVHWVSVGKQDKSGLLMKLQNLCTRLDQDESFSQRLPLNIEEAKDRLRILMLRKHPRSLL
ILDDVWDSWVLKAFDSQCQILLTTRDKSVTDSVMGPKYVVPVESSLGKEKGLEILSLFVN
MKKADLPEQAHSIIKECKGSPLVVSLIGALLRDFPNRWEYYLKQLQNKQFKRIRKSSSYD
YEALDEAMSISVEMLREDIKDYYTDLSILQKDVKVPTKVLCILWDMETEEVEDILQEFVN
KSLLFCDRNGKSFRYYLHDLQVDFLTEKNCSQLQDLHKKIITQFQRYHQPHTLSPDQEDC
MYWYNFLAYHMASAKMHKELCALMFSLDWIKAKTELVGPAHLIHEFVEYRHILDEKDCAV
SENFQEFLSLNGHLLGRQPFPNIVQLGLCEPETSEVYQQAKLQAKQEVDNGMLYLEWINK
KNITNLSRLVVRPHTDAVYHACFSEDGQRIASCGADKTLQVFKAETGEKLLEIKAHEDEV
LCCAFSTDDRFIATCSVDKKVKIWNSMTGELVHTYDEHSEQVNCCHFTNSSHHLLLATGS
SDCFLKLWDLNQKECRNTMFGHTNSVNHCRFSPDDKLLASCSADGTLKLWDATSANERKS
INVKQFFLNLEDPQEDMEVIVKCCSWSADGARIMVAAKNKIFLFDIHTSGLLGEIHTGHH
STIQYCDFSPQNHLAVVALSQYCVELWNTDSRSKVADCRGHLSWVHGVMFSPDGSSFLTS
SDDQTIRLWETKKVCKNSAVMLKQEVDVVFQENEVMVLAVDHIRRLQLINGRTGQIDYLT
EAQVSCCCLSPHLQYIAFGDENGAIEILELVNNRIFQSRFQHKKTVWHIQFTADEKTLIS
SSDDAEIQVWNWQLDKCIFLRGHQETVKDFRLLKNSRLLSWSFDGTVKVWNIITGNKEKD
FVCHQGTVLSCDISHDATKFSSTSADKTAKIWSFDLLLPLHELRGHNGCVRCSAFSVDST
LLATGDDNGEIRIWNVSNGELLHLCAPLSEEGAATHGGWVTDLCFSPDGKMLISAGGYIK
WWNVVTGESSQTFYTNGTNLKKIHVSPDFKTYVTVDNLGILYILQTLE

Sequence of entity 2 (B, D, F, H, J, L, N), FASTA

>5WVE_2 Cytochrome c (chains B, D, F, H, J, L, N)
MGDVEKGKKIFVQKCAQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGFTYTDANKNKGITW
KEETLMEYLENPKKYIPGTKMIFAGIKKKTEREDLIAYLKKATNE

Sequence of entity 3 (O, P, Q, R, W, X), FASTA

>5WVE_3 Apoptotic protease-activating factor 1 (chains O, P, Q, R, W, X)
MDAKARNCLLQHREALEKDIKTSYIMDHMISDGFLTISEEEKVRNEPTQQQRAAMLIKMI
LKKDNDSYVSFYNALLHEGYKDLAALLHDGIPVVSSSSGKDS

Sequence of entity 4 (S, T, U, V, Y), FASTA

>5WVE_4 Caspase (chains S, T, U, V, Y)
MDEADRRLLRRCRLRLVEELQVDQLWDVLLSRELFRPHMIEDIQRAGSGSRRDQARQLII
DLETRGSQALPLFISCLEDTGQDMLASFLRTNRQAAKLSK

Ligands and cofactors

ID	Name	Formula	Copies
HEM	Protoporphyrin IX containing FE	C34 H32 Fe N4 O4	7
MG	Magnesium ion	Mg	7
DTP	2'-deoxyadenosine 5'-triphosphate	C10 H16 N5 O12 P3	7

Primary citation

Mechanistic insights into caspase-9 activation by the structure of the apoptosome holoenzyme. Li, Y., Zhou, M., Hu, Q. et al. Proc Natl Acad Sci U S A (2017) 114:1542-1547. DOI 10.1073/pnas.1620626114 · 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
3YGS 2.5 Å, Apaf-1 card in complex with prodomain of procaspase-9
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
3J2T 9.5 Å, An improved model of the human apoptosome
1C15 Solution structure of apaf-1 card

Browse structure collections

About this viewer

MolViewer shows 5WVE directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.