5JUY: Active human apoptosome with procaspase-9

Active human apoptosome with procaspase-9. Determined by electron microscopy at 4.1 Å resolution. Released 19 Oct 2016.

Method: Electron microscopy
Resolution: 4.1 Å
Organisms: Homo sapiens, Bos taurus
Chains: 18
Atoms: 76,058
Mol. weight: 1127.68 kDa
Ligands: DTP, HEC
Released: 19 Oct 2016

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

Secondary structure: helices and β-sheets

5JUY contains 344 α-helices and 525 β-strands across 18 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 and F: 33 helices, 71 β-strands

Element	Residues	Length	Sheet
α-helix	108-113	6
α-helix	120-122	3
α-helix	130-141	12
β-strand	148-153	6	1
α-helix	161-165	5
α-helix	171-177	7
β-strand	182-186	5	1
α-helix	192-206	15
α-helix	220-233	14
β-strand	239-243	5	1
α-helix	248-253	6
β-strand	259-264	6	1
β-strand	279	1	1
α-helix	288-299	12
α-helix	303-305	3
α-helix	309-317	9
α-helix	321-333	13
α-helix	338-344	7
α-helix	364-373	10
α-helix	380-384	5
α-helix	385-388	4
α-helix	389-390	2
β-strand	395	1	2
α-helix	398-404	7
α-helix	408-420	13
β-strand	425-428	4	2
β-strand	433-436	4	2
α-helix	439-448	10
α-helix	453-467	15
β-strand	469	1	3
β-strand	472	1	3
α-helix	480-493	14
α-helix	497-504	8
α-helix	507-516	10
α-helix	519-529	11
α-helix	535-551	17
α-helix	563-567	5
α-helix	575-586	12
β-strand	596	1	4
α-helix	599-601	3
β-strand	609-611	3	5
β-strand	618-620	3	6
β-strand	623	1	7
β-strand	629-632	4	7
β-strand	633-634	2	6
β-strand	638-643	6	7
β-strand	649-654	6	7
β-strand	660-663	4	8
β-strand	671-676	6	8
β-strand	681-685	5	8
β-strand	691-695	5	8
β-strand	715-719	5	9
β-strand	725-729	5	9
β-strand	735-739	5	9
β-strand	748-751	4	10
β-strand	757-761	5	10
β-strand	766-771	6	10
β-strand	777-782	6	10
β-strand	801-806	6	11
β-strand	813-817	5	11
β-strand	820-824	5	11
β-strand	831-835	5	11
α-helix	841-843	3
β-strand	845-848	4	12
β-strand	854-858	5	12
β-strand	864-868	5	12
β-strand	874-878	5	12
β-strand	885-891	7	5
β-strand	896-901	6	5
β-strand	906-910	5	5
α-helix	911-914	4
β-strand	922-931	10	13
β-strand	934-941	8	13
β-strand	946-949	4	13
β-strand	956-959	4	13
β-strand	966-969	4	14
α-helix	970	1
β-strand	975-979	5	14
β-strand	985-989	5	14
β-strand	996-999	4	14
α-helix	1005	1
β-strand	1006-1010	5	15
β-strand	1018-1022	5	15
β-strand	1026-1031	6	15
β-strand	1036-1041	6	15
β-strand	1049-1052	4	16
β-strand	1058-1061	4	16
β-strand	1067-1070	4	16
β-strand	1080-1081	2	16
β-strand	1089-1093	5	17
β-strand	1101-1104	4	17
β-strand	1109-1112	4	17
β-strand	1121-1123	3	17
β-strand	1132-1135	4	18
β-strand	1142-1145	4	18
β-strand	1151-1154	4	18
β-strand	1184-1185	2	19
β-strand	1191-1195	5	19
β-strand	1199-1203	5	19
β-strand	1210	1	19
β-strand	1224-1225	2	20
β-strand	1232-1235	4	20
β-strand	1241-1244	4	20
β-strand	1245	1	4

Chains B, D, E and G: 42 helices, 71 β-strands

Element	Residues	Length	Sheet
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
α-helix	108-113	6
α-helix	120-122	3
α-helix	130-141	12
β-strand	148-153	6	21
α-helix	161-165	5
α-helix	171-177	7
β-strand	182-186	5	21
α-helix	192-206	15
α-helix	220-233	14
β-strand	239-243	5	21
α-helix	248-253	6
β-strand	259-264	6	21
β-strand	279	1	21
α-helix	288-299	12
α-helix	303-305	3
α-helix	309-317	9
α-helix	321-333	13
α-helix	338-344	7
α-helix	364-373	10
α-helix	380-384	5
α-helix	385-388	4
α-helix	389-390	2
β-strand	395	1	22
α-helix	398-404	7
α-helix	408-420	13
β-strand	425-428	4	22
β-strand	433-436	4	22
α-helix	439-448	10
α-helix	453-467	15
β-strand	469	1	23
β-strand	472	1	23
α-helix	480-493	14
α-helix	497-504	8
α-helix	507-516	10
α-helix	519-529	11
α-helix	535-551	17
α-helix	563-567	5
α-helix	575-586	12
β-strand	596	1	24
α-helix	599-601	3
β-strand	609-611	3	25
β-strand	618-620	3	26
β-strand	623	1	27
β-strand	629-632	4	27
β-strand	633-634	2	26
β-strand	638-643	6	27
β-strand	649-654	6	27
β-strand	660-663	4	28
β-strand	671-676	6	28
β-strand	681-685	5	28
β-strand	691-695	5	28
β-strand	715-719	5	29
β-strand	725-729	5	29
β-strand	735-739	5	29
β-strand	748-751	4	30
β-strand	757-761	5	30
β-strand	766-771	6	30
β-strand	777-782	6	30
β-strand	801-806	6	31
β-strand	813-817	5	31
β-strand	820-824	5	31
β-strand	831-835	5	31
α-helix	841-843	3
β-strand	845-848	4	32
β-strand	854-858	5	32
β-strand	864-868	5	32
β-strand	874-878	5	32
β-strand	885-891	7	25
β-strand	896-901	6	25
β-strand	906-910	5	25
α-helix	911-914	4
β-strand	922-931	10	33
β-strand	934-941	8	33
β-strand	946-949	4	33
β-strand	956-959	4	33
β-strand	966-969	4	34
α-helix	970	1
β-strand	975-979	5	34
β-strand	985-989	5	34
β-strand	996-999	4	34
α-helix	1005	1
β-strand	1006-1010	5	35
β-strand	1018-1022	5	35
β-strand	1026-1031	6	35
β-strand	1036-1041	6	35
β-strand	1049-1052	4	36
β-strand	1058-1061	4	36
β-strand	1067-1070	4	36
β-strand	1080-1081	2	36
β-strand	1089-1093	5	37
β-strand	1101-1104	4	37
β-strand	1109-1112	4	37
β-strand	1121-1123	3	37
β-strand	1132-1135	4	38
β-strand	1142-1145	4	38
β-strand	1151-1154	4	38
β-strand	1184-1185	2	39
β-strand	1191-1195	5	39
β-strand	1199-1203	5	39
β-strand	1210	1	39
β-strand	1224-1225	2	40
β-strand	1232-1235	4	40
β-strand	1241-1244	4	40
β-strand	1245	1	24

Chains H, I, J, K, L, M and N: 7 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	3-13	11
β-strand	19	1	141
α-helix	24-26	3
α-helix	30	1
β-strand	31	1	141
β-strand	39	1	142
α-helix	50-53	4
β-strand	58	1	142
α-helix	63-67	5
α-helix	71-74	4
α-helix	88-101	14

Chains O, P, Q and R: 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	69-79	11
α-helix	83-93	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Apoptotic protease-activating factor 1	A, B, C, D, E, F, G	protein	1248	Homo sapiens	O14727 (AlphaFold model)
Cytochrome c	H, I, J, K, L, M, N	protein	104	Bos taurus	P62894 (AlphaFold model)
Caspase-9	O, P, Q, R	protein	95	Homo sapiens	P55211 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F, G), FASTA

>5JUY_1 Apoptotic protease-activating factor 1 (chains A, B, C, D, E, F, G)
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 (H, I, J, K, L, M, N), FASTA

>5JUY_2 Cytochrome c (chains H, I, J, K, L, M, N)
GDVEKGKKIFVQKCAQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGFSYTDANKNKGITWG
EETLMEYLENPKKYIPGTKMIFAGIKKKGEREDLIAYLKKATNE

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

>5JUY_3 Caspase-9 (chains O, P, Q, R)
MDEADRRLLRRCRLRLVEELQVDQLWDALLSRELFRPHMIEDIQRAGSGSRRDQARQLII
DLETRGSQALPLFISCLEDTGQDMLASFLRTNRQA

Ligands and cofactors

ID	Name	Formula	Copies
DTP	2'-deoxyadenosine 5'-triphosphate	C10 H16 N5 O12 P3	7
HEC	Heme C	C34 H36 Fe N4 O4	7

Primary citation

A near atomic structure of the active human apoptosome. Cheng, T.C., Hong, C., Akey, I.V. et al. Elife (2016) 5. DOI 10.7554/eLife.17755 · 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
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

Browse structure collections

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