3JBT: Atomic structure of the Apaf-1 apoptosome

Atomic structure of the Apaf-1 apoptosome. Determined by electron microscopy at 3.8 Å resolution. Released 18 Nov 2015.

Method: Electron microscopy
Resolution: 3.8 Å
Organisms: Homo sapiens, Equus caballus
Chains: 14
Atoms: 70,252
Mol. weight: 1096.45 kDa
Ligands: DTP, HEM, MG
Released: 18 Nov 2015

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

Secondary structure: helices and β-sheets

3JBT contains 280 α-helices and 539 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, C, E, G, I, 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	507-516	10
α-helix	521-532	12
α-helix	535-549	15
α-helix	551-554	4
α-helix	563-566	4
α-helix	576-590	15
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

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Apoptotic protease-activating factor 1	A, C, E, G, I, K, M	protein	1260	Homo sapiens	O14727 (AlphaFold model)
Cytochrome c	B, D, F, H, J, L, N	protein	105	Equus caballus	P00004 (AlphaFold model)

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

>3JBT_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
WWNVVTGESSQTFYTNGTNLKKIHVSPDFKTYVTVDNLGILYILQTLELEHHHHHHHHHH

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

>3JBT_2 Cytochrome c (chains B, D, F, H, J, L, N)
MGDVEKGKKIFVQKCAQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGFTYTDANKNKGITW
KEETLMEYLENPKKYIPGTKMIFAGIKKKTEREDLIAYLKKATNE

Ligands and cofactors

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

Primary citation

Atomic structure of the apoptosome: mechanism of cytochrome c- and dATP-mediated activation of Apaf-1. Zhou, M., Li, Y., Hu, Q. et al. Genes Dev (2015) 29:2349-2361. DOI 10.1101/gad.272278.115 · 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
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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