3J2T: An improved model of the human apoptosome

An improved model of the human apoptosome. Determined by electron microscopy at 9.5 Å resolution. Released 10 Apr 2013.

Method: Electron microscopy
Resolution: 9.5 Å
Organisms: Homo sapiens, Bos taurus
Chains: 14
Atoms: 70,189
Mol. weight: 1097.7 kDa
Ligands: ATP, HEM
Released: 10 Apr 2013

Explore 3J2T in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3J2T contains 294 α-helices and 497 β-strands across 14 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, B, C, D, E, F and G: 36 helices, 69 β-strands

Element	Residues	Length	Sheet
α-helix	108-113	6
α-helix	130-140	11
α-helix	141-143	3
β-strand	149-153	5	1
α-helix	160-167	8
α-helix	171-175	5
β-strand	182-186	5	1
α-helix	192-205	14
α-helix	220-233	14
β-strand	239-245	7	1
α-helix	248-251	4
β-strand	260-264	5	1
α-helix	267-272	6
β-strand	277-279	3	1
α-helix	288-299	12
α-helix	303-305	3
α-helix	308-317	10
α-helix	321-333	13
α-helix	338-348	11
α-helix	364-373	10
α-helix	377-385	9
α-helix	386-388	3
α-helix	390	1
β-strand	395	1	2
α-helix	397-400	4
α-helix	401-404	4
α-helix	408-420	13
β-strand	425-429	5	2
β-strand	432-436	5	2
α-helix	439-448	10
α-helix	452-467	16
α-helix	482-493	12
α-helix	497-504	8
α-helix	507-516	10
α-helix	519-528	10
α-helix	529-531	3
α-helix	535-547	13
α-helix	563-566	4
α-helix	567-569	3
α-helix	575-586	12
β-strand	595-597	3	3
β-strand	609-611	3	4
β-strand	618-623	6	5
β-strand	629-634	6	5
β-strand	639-643	5	5
β-strand	649-653	5	5
β-strand	660-665	6	6
β-strand	671-676	6	6
β-strand	681-685	5	6
β-strand	691-695	5	6
β-strand	702-707	6	7
β-strand	715-720	6	7
β-strand	725-729	5	7
β-strand	735-739	5	7
β-strand	746-751	6	8
β-strand	757-762	6	8
β-strand	766-771	6	8
β-strand	776-782	7	8
α-helix	797-798	2
β-strand	801-806	6	9
β-strand	812-817	6	9
β-strand	820-825	6	9
β-strand	831-836	6	9
β-strand	845-848	4	10
β-strand	854-860	7	10
β-strand	863-868	6	10
β-strand	873-878	6	10
α-helix	884	1
β-strand	885-890	6	4
β-strand	896-901	6	4
β-strand	906-910	5	4
α-helix	911-914	4
β-strand	926-931	6	11
β-strand	934-940	7	11
β-strand	946-950	5	11
β-strand	956-959	4	11
β-strand	966-969	4	12
α-helix	970	1
β-strand	975-979	5	12
β-strand	986-989	4	12
β-strand	996-998	3	12
β-strand	1009-1011	3	13
β-strand	1018-1020	3	13
β-strand	1026-1031	6	13
β-strand	1036-1041	6	13
β-strand	1047-1052	6	14
β-strand	1057-1062	6	14
β-strand	1066-1071	6	14
β-strand	1079-1082	4	14
β-strand	1092-1093	2	15
β-strand	1101-1102	2	15
β-strand	1107	1	16
β-strand	1109-1112	4	15
β-strand	1121-1123	3	15
β-strand	1130	1	16
β-strand	1132-1135	4	17
β-strand	1141-1145	5	17
β-strand	1151-1155	5	17
β-strand	1182-1185	4	18
β-strand	1191-1195	5	18
β-strand	1200-1203	4	18
β-strand	1208	1	18
β-strand	1223-1225	3	3
β-strand	1231-1235	5	3
β-strand	1241-1246	6	3

Chains H, I, J, K, L, M 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	127
α-helix	50-54	5
β-strand	58	1	127
α-helix	61-69	9
α-helix	71-74	4
α-helix	88-101	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Apoptotic protease-activating factor 1	A, B, C, D, E, F, G	protein	1263	Homo sapiens	O14727 (AlphaFold model)
Cytochrome c	H, I, J, K, L, M, N	protein	104	Bos taurus	P62894 (AlphaFold model)

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

>3J2T_1 Apoptotic protease-activating factor 1 (chains A, B, C, D, E, F, G)
HHHHHHMDAKARNCLLQHREALEKDIKTSYIMDHMISDGFLTISEEEKVRNEPTQQQRAA
MLIKMILKKDNDSYVSFYNALLHEGYKDLAALLHDGIPVVSSSSGKDSVSGITSYVRTVL
CEGGVPQRPVVFVTRKKLVNAIQQKLSKLKGEPGWVTIHGMAGCGKSVLAAEAVRDHSLL
EGCFPGGVHWVSVGKQDKSGLLMKLQNLCTRLDQDESFSQRLPLNIEEAKDRLRILMLRK
HPRSLLILDDVWDSWVLKAFDSQCQILLTTRDKSVTDSVMGPKYVVPVESSLGKEKGLEI
LSLFVNMKKADLPEQAHSIIKECKGSPLVVSLIGALLRDFPNRWEYYLKQLQNKQFKRIR
KSSSYDYEALDEAMSISVEMLREDIKDYYTDLSILQKDVKVPTKVLCILWDMETEEVEDI
LQEFVNKSLLFCDRNGKSFRYYLHDLQVDFLTEKNCSQLQDLHKKIITQFQRYHQPHTLS
PDQEDCMYWYNFLAYHMASAKMHKELCALMFSLDWIKAKTELVGPAHLIHEFVEYRHILD
EKDCAVSENFQEFLSLNGHLLGRQPFPNIVQLGLCEPETSEVYQQAKLQAKQEVDNGMLY
LEWINKKNITNLSRLVVRPHTDAVYHACFSEDGQRIASCGADKTLQVFKAETGEKLLEIK
AHEDEVLCCAFSTDDRFIATCSVDKKVKIWNSMTGELVHTYDEHSEQVNCCHFTNSSHHL
LLATGSSDCFLKLWDLNQKECRNTMFGHTNSVNHCRFSPDDKLLASCSADGTLKLWDATS
ANERKSINVKQFFLNLEDPQEDMEVIVKCCSWSADGARIMVAAKNKIFLFDIHTSGLLGE
IHTGHHSTIQYCDFSPQNHLAVVALSQYCVELWNTDSRSKVADCRGHLSWVHGVMFSPDG
SSFLTSSDDQTIRLWETKKVCKNSAVMLKQEVDVVFQENEVMVLAVDHIRRLQLINGRTG
QIDYLTEAQVSCCCLSPHLQYIAFGDENGAIEILELVNNRIFQSRFQHKKTVWHIQFTAD
EKTLISSSDDAEIQVWNWQLDKCIFLRGHQETVKDFRLLKNSRLLSWSFDGTVKVWNIIT
GNKEKDFVCHQGTVLSCDISHDATKFSSTSADKTAKIWSFDLLLPLHELRGHNGCVRCSA
FSVDSTLLATGDDNGEIRIWNVSNGELLHLCAPLSEEGAATHGGWVTDLCFSPDGKMLIS
AGGYIKWWNVVTGESSQTFYTNGTNLKKIHVSPDFKTYVTVDNLGILYILQTLEHHHHHH
HHH

Sequence of entity 2 (H, I, J, K, L, M, N), FASTA

>3J2T_2 Cytochrome c (chains H, I, J, K, L, M, N)
GDVEKGKKIFVQKCAQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGFSYTDANKNKGITWG
EETLMEYLENPKKYIPGTKMIFAGIKKKGEREDLIAYLKKATNE

Ligands and cofactors

ID	Name	Formula	Copies
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	7
HEM	Protoporphyrin IX containing FE	C34 H32 Fe N4 O4	7

Primary citation

Changes in apaf-1 conformation that drive apoptosome assembly. Yuan, S., Topf, M., Reubold, T.F. et al. Biochemistry (2013) 52:2319-2327. DOI 10.1021/bi301721g · 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
5WVE 4.4 Å, Apaf-1-Caspase-9 holoenzyme
1C15 Solution structure of apaf-1 card

Browse structure collections

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