3V3K: Human caspase 9

Human caspase 9 in complex with bacterial effector protein. Determined by X-ray diffraction at 3.49 Å resolution. Released 6 Mar 2013.

Method: X-ray diffraction
Resolution: 3.49 Å
Organisms: Homo sapiens, Escherichia coli O157:H7
Chains: 16
Atoms: 25,428
Mol. weight: 394.26 kDa
Released: 6 Mar 2013

Explore 3V3K in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3V3K contains 141 α-helices and 179 β-strands across 16 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 A: 10 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	152	1	1
β-strand	163-169	7	2
α-helix	176-178	3
α-helix	182-195	14
β-strand	198-204	7	2
α-helix	208-219	12
β-strand	230-235	6	2
β-strand	238-239	2	3
β-strand	240C	1	4
β-strand	242-244	3	3
β-strand	255-257	3	3
α-helix	258-263	6
α-helix	271-273	3
β-strand	278-283	6	2
β-strand	289	1	5
α-helix	290	1
β-strand	291	1	6
β-strand	294-295	2	7
β-strand	321	1	8
β-strand	327-331	5	2
β-strand	337	1	5
α-helix	338-339	2
β-strand	340-342	3	9
β-strand	346-347	2	9
α-helix	348-360	13
α-helix	366-378	13
β-strand	384	1	6
β-strand	388-392	4	2
β-strand	397	1	1
α-helix	399-401	3

Chain B: 9 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	34-36	3
α-helix	38-39	2
α-helix	40-55	16
α-helix	63-83	21
β-strand	84-87	4	10
β-strand	95-98	4	10
α-helix	99	1
α-helix	104-127	24
α-helix	137-141	5
α-helix	149-161	13
α-helix	173-175	3
β-strand	187-188	2	9

Chain C: 9 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	152	1	11
β-strand	163-169	7	2
α-helix	176-178	3
α-helix	182-195	14
β-strand	198-204	7	2
α-helix	208-220	13
β-strand	229-235	7	2
β-strand	238-239	2	12
β-strand	240C	1	4
β-strand	242-244	3	12
α-helix	245	1
β-strand	255-257	3	12
α-helix	258-263	6
α-helix	271-273	3
β-strand	278-283	6	2
β-strand	289	1	13
β-strand	291	1	14
β-strand	294	1	8
β-strand	320-321	2	7
β-strand	327-331	5	2
β-strand	337	1	13
α-helix	338-339	2
β-strand	340-342	3	15
β-strand	346-347	2	15
α-helix	348-360	13
α-helix	366-378	13
β-strand	384	1	14
β-strand	388-393	5	2
β-strand	397	1	11

Chain D: 8 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	34-36	3
α-helix	38-39	2
α-helix	40-55	16
α-helix	63-83	21
β-strand	84-87	4	16
β-strand	95-98	4	16
α-helix	99	1
α-helix	104-127	24
α-helix	137-141	5
α-helix	149-162	14
β-strand	187-188	2	15

Chain E: 8 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	152	1	17
β-strand	163-169	7	18
α-helix	176-178	3
α-helix	182-195	14
β-strand	198-204	7	18
α-helix	208-219	12
β-strand	230-235	6	18
β-strand	240C	1	19
β-strand	242-244	3	20
β-strand	255-257	3	20
α-helix	258-262	5
α-helix	271-273	3
β-strand	278-283	6	18
β-strand	289	1	21
β-strand	291	1	22
β-strand	294-295	2	23
β-strand	320-321	2	24
β-strand	327-331	5	18
β-strand	337	1	21
α-helix	338-339	2
β-strand	340-342	3	25
β-strand	346-347	2	25
α-helix	348-360	13
α-helix	366-378	13
β-strand	384	1	22
β-strand	388-393	5	18
β-strand	397	1	17

Chains F and J: 9 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	34-36	3
α-helix	38-39	2
α-helix	40-55	16
α-helix	63-83	21
β-strand	84-87	4	26
β-strand	95-98	4	26
α-helix	99	1
α-helix	104-127	24
α-helix	137-141	5
α-helix	149-161	13
α-helix	172-175	4
β-strand	187-188	2	25

Chain G: 8 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	152	1	27
β-strand	163-169	7	18
α-helix	176-178	3
α-helix	182-195	14
β-strand	198-204	7	18
α-helix	208-220	13
β-strand	230-235	6	18
β-strand	238-239	2	28
β-strand	240C	1	19
β-strand	242-244	3	28
β-strand	255-257	3	28
α-helix	258-264	7
α-helix	271-273	3
β-strand	278-283	6	18
β-strand	289	1	29
β-strand	291	1	30
β-strand	294-295	2	24
β-strand	320-321	2	23
β-strand	327-331	5	18
β-strand	337	1	29
α-helix	338-339	2
β-strand	340-342	3	31
β-strand	346-347	2	31
α-helix	348-360	13
α-helix	366-378	13
β-strand	384	1	30
β-strand	388-393	5	18
β-strand	397	1	27

Chain H: 9 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	34-36	3
α-helix	38-39	2
α-helix	40-55	16
α-helix	63-83	21
β-strand	84-87	4	32
β-strand	95-98	4	32
α-helix	99	1
α-helix	104-127	24
α-helix	139-142	4
α-helix	149-161	13
α-helix	172-174	3
β-strand	187-188	2	31

6 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
Caspase-9	A, C, E, G, I, K, M, O	protein	276	Homo sapiens	P55211 (AlphaFold model)
Putative uncharacterized protein ECs1815	B, D, F, H, J, L, N, P	protein	165	Escherichia coli O157:H7	Q8XAL7 (AlphaFold model)

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

>3V3K_1 Caspase-9 (chains A, C, E, G, I, K, M, O)
ALESLRGNADLAYILSMEPCGHCLIINNVNFCRESGLRTRTGSNIDCEKLRRRFSSLHFM
VEVKGDLTAKKMVLALLELARQDHGALDCCVVVILSHGCQASHLQFPGAVYGTDGCPVSV
EKIVNIFNGTSCPSLGGKPKLFFIQACGGEQKDHGFEVASTSPEDESPGSNPEPDATPFQ
EGLRTFDQLDAISSLPTPSDIFVSYSTFPGFVSWRDPKSGSWYVETLDDIFEQWAHSEDL
QSLLLRVANAVSVKGIYKQMPGCFNFLRKKLFFKTS

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

>3V3K_2 Putative uncharacterized protein ECs1815 (chains B, D, F, H, J, L, N, P)
TPESVSELNHNHFLSPELQDKLDVMVSIYSCARNNNELEEIFQELSAFVSGLMDKRNSVF
EVRNENTDEVVGALRAGMTIEDRDSYIRDLFFLHSLKVKIEESRQGKEDSKCKVYNLLCP
HHSSELYGDLRAMKCLVEGCSDDFNPFDIIRVPDLTYNKGSLQCG

Primary citation

Human caspase 9 in complex with bacterial effector protein. Moertl, M., Maskos, K., Steuber, H. PLoS One (2013).

Other PDB entries of the same protein (UniProt P55211 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3D9T 1.5 Å, CIAP1-BIR3 in complex with N-terminal peptide from Caspase-9 (ATPFQE)
4RHW 2.1 Å, Crystal structure of Apaf-1 CARD and caspase-9 CARD complex
1NW9 2.4 Å, Structure of caspase-9 in an inhibitory complex with xiap-BIR3
9R44 2.46 Å, Crystal structure of human caspase-9 CARD
3YGS 2.5 Å, Apaf-1 card in complex with prodomain of procaspase-9
1JXQ 2.8 Å, Structure of cleaved, CARD domain deleted Caspase-9
2AR9 2.8 Å, Crystal structure of a dimeric caspase-9
5WVC 2.99 Å, Structure of the CARD-CARD disk
9S6F 3.3 Å, Cryo-EM structure of human caspase-9 CARD (WT) filament
9S6E 3.5 Å, Cryo-EM structure of human caspase-9 CARD (H38R) mutant filament
5JUY 4.1 Å, Active human apoptosome with procaspase-9
5WVE 4.4 Å, Apaf-1-Caspase-9 holoenzyme

Browse structure collections

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