9CPN: PDB entry 9CPN

Name: PDB 9CPN: Structural basis of BAK sequestration by MCL-1 and consequences for apoptosis initiation
Published: 2025-06-04
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: apoptosis

Structural basis of BAK sequestration by MCL-1 and consequences for apoptosis initiation. Determined by X-ray diffraction at 1.89 Å resolution. Released 4 Jun 2025.

Method: X-ray diffraction
Resolution: 1.89 Å
Organisms: synthetic construct, Homo sapiens
Chains: 8
Atoms: 17,760
Mol. weight: 240.31 kDa
Released: 4 Jun 2025

Explore 9CPN in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9CPN contains 136 α-helices and 97 β-strands across 8 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: 32 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	810-814	5	1
α-helix	821-835	15
β-strand	838-842	5	1
α-helix	847-856	10
β-strand	863-867	5	1
α-helix	868-870	3
α-helix	871-876	6
β-strand	880	1	2
α-helix	881-883	3
α-helix	887-890	4
β-strand	893	1	3
α-helix	895-900	6
β-strand	902-903	2	4
β-strand	906-907	2	4
β-strand	910-915	6	1
β-strand	918-922	5	5
β-strand	932	1	6
α-helix	933-935	3
α-helix	936-945	10
β-strand	949-951	3	5
α-helix	962-967	6
β-strand	971-976	6	7
β-strand	979-986	8	7
α-helix	990-1004	15
α-helix	1014-1022	9
β-strand	1026-1031	6	5
α-helix	1033-1035	3
α-helix	1036-1042	7
β-strand	1046-1049	4	5
α-helix	1050-1052	3
β-strand	1053	1	6
β-strand	1054	1	8
β-strand	1057	1	8
α-helix	1061	1
β-strand	1062-1063	2	9
β-strand	1064-1070	7	1
β-strand	1071	1	2
α-helix	1077-1082	6
α-helix	1083-1088	6
α-helix	1091-1100	10
β-strand	1105-1106	2	1
β-strand	1108	1	3
α-helix	1109-1115	7
α-helix	1119-1130	12
β-strand	1132-1133	2	9
α-helix	1134-1135	2
α-helix	1140-1156	17
α-helix	1161-1166	6
α-helix	1168-1191	24
α-helix	1203-1223	21
α-helix	1225-1235	11
α-helix	1240-1254	15
α-helix	1261-1280	20
α-helix	1284-1286	3
α-helix	1287-1308	22
α-helix	1311-1318	8

Chain B: 33 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	811-814	4	10
α-helix	821-835	15
β-strand	839-842	4	10
α-helix	847-854	8
β-strand	863-867	5	10
α-helix	868-870	3
α-helix	871-876	6
β-strand	880	1	11
α-helix	881-883	3
α-helix	887-890	4
β-strand	893	1	12
α-helix	895-900	6
β-strand	902-903	2	13
β-strand	906-907	2	13
β-strand	910-915	6	10
β-strand	918-922	5	14
β-strand	932	1	15
α-helix	933-935	3
α-helix	936-944	9
β-strand	949-951	3	14
α-helix	958-967	10
β-strand	971	1	16
β-strand	986	1	16
α-helix	990-1004	15
α-helix	1014-1022	9
β-strand	1026-1031	6	14
α-helix	1033-1035	3
α-helix	1036-1042	7
β-strand	1046-1049	4	14
α-helix	1050-1052	3
β-strand	1053-1054	2	15
β-strand	1057-1058	2	15
α-helix	1061	1
β-strand	1062-1063	2	17
β-strand	1064-1070	7	10
β-strand	1071	1	11
α-helix	1077-1083	7
α-helix	1084-1088	5
α-helix	1091-1100	10
β-strand	1105-1106	2	10
β-strand	1108	1	12
α-helix	1109-1115	7
α-helix	1119-1130	12
β-strand	1132-1133	2	17
α-helix	1134-1135	2
α-helix	1140-1156	17
α-helix	1161-1191	31
α-helix	1205-1223	19
α-helix	1225-1235	11
α-helix	1242-1245	4
α-helix	1247-1254	8
α-helix	1261-1280	20
α-helix	1284-1286	3
α-helix	1287-1301	15
α-helix	1303-1308	6
α-helix	1311-1318	8

Chain C: 33 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	811-814	4	18
α-helix	821-835	15
β-strand	839-842	4	18
α-helix	847-855	9
β-strand	863-867	5	18
α-helix	868-870	3
α-helix	871-876	6
β-strand	880	1	19
α-helix	881-883	3
α-helix	887-890	4
β-strand	893	1	20
α-helix	895-900	6
β-strand	902-903	2	21
β-strand	906-907	2	21
β-strand	910-915	6	18
β-strand	918-922	5	22
β-strand	932	1	23
α-helix	933-935	3
α-helix	936-944	9
β-strand	949-951	3	22
α-helix	958-967	10
β-strand	971	1	24
β-strand	974-976	3	25
β-strand	979-981	3	25
β-strand	986	1	24
α-helix	990-1004	15
α-helix	1014-1022	9
β-strand	1026-1031	6	22
α-helix	1033-1035	3
α-helix	1036-1042	7
β-strand	1046-1049	4	22
α-helix	1050-1052	3
β-strand	1053-1054	2	23
β-strand	1057-1058	2	23
α-helix	1061	1
β-strand	1062-1063	2	26
β-strand	1064-1070	7	18
β-strand	1071	1	19
α-helix	1077-1083	7
α-helix	1084-1088	5
α-helix	1091-1100	10
β-strand	1105-1106	2	18
β-strand	1108	1	20
α-helix	1109-1115	7
α-helix	1119-1130	12
β-strand	1132-1133	2	26
α-helix	1134-1135	2
α-helix	1140-1156	17
α-helix	1161-1191	31
α-helix	1204-1212	9
α-helix	1213-1217	5
α-helix	1218-1223	6
α-helix	1225-1235	11
α-helix	1240-1252	13
α-helix	1261-1280	20
α-helix	1284-1286	3
α-helix	1287-1308	22
α-helix	1311-1318	8

Chain D: 34 helices, 25 β-strands

Element	Residues	Length	Sheet
α-helix	806-807	2
β-strand	811-814	4	27
α-helix	821-835	15
β-strand	839-842	4	27
α-helix	847-856	10
β-strand	863-867	5	27
α-helix	868-870	3
α-helix	871-876	6
β-strand	880	1	28
α-helix	881-883	3
α-helix	887-890	4
β-strand	893	1	29
α-helix	895-900	6
β-strand	902-903	2	30
β-strand	906-907	2	30
β-strand	910-915	6	27
β-strand	918-922	5	31
β-strand	932	1	32
α-helix	933-935	3
α-helix	936-944	9
β-strand	949-951	3	31
α-helix	958-967	10
β-strand	971	1	33
β-strand	974	1	34
β-strand	981	1	34
β-strand	986	1	33
α-helix	990-1004	15
α-helix	1014-1022	9
β-strand	1026-1031	6	31
α-helix	1033-1035	3
α-helix	1036-1042	7
β-strand	1046-1049	4	31
α-helix	1050-1052	3
β-strand	1053-1054	2	32
β-strand	1057-1058	2	32
α-helix	1061	1
β-strand	1062-1063	2	35
β-strand	1064-1070	7	27
β-strand	1071	1	28
α-helix	1077-1083	7
α-helix	1084-1088	5
α-helix	1091-1100	10
β-strand	1105-1106	2	27
β-strand	1108	1	29
α-helix	1109-1115	7
α-helix	1119-1130	12
β-strand	1132-1133	2	35
α-helix	1134-1135	2
α-helix	1140-1156	17
α-helix	1161-1191	31
α-helix	1205-1223	19
α-helix	1225-1235	11
α-helix	1240-1245	6
α-helix	1247-1254	8
α-helix	1261-1280	20
α-helix	1284-1286	3
α-helix	1287-1301	15
α-helix	1303-1308	6
α-helix	1311-1318	8

Chains E, F, G and H: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	70-88	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Induced myeloid leukemia cell differentiation protein Mcl-1	A, B, C, D	protein	517	synthetic construct
Bcl-2 homologous antagonist/killer	E, F, G, H	protein	22	Homo sapiens	Q16611 (AlphaFold model)

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

>9CPN_1 Induced myeloid leukemia cell differentiation protein Mcl-1 (chains A, B, C, D)
AIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDII
FWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKD
LLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIKD
VGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSKV
NYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLG
AVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDEA
LKDAQTGSELYRQSLEIISRYLREQATGAADTAPMGRSGATSRKALETLRRVGDGVQRNH
ETAFQGMLRKLDIKNEDDVKSLSRVMIHVFSDGVTNWGRIVTLISFGAFVAKHLKTINQE
SCIEPLAESITDVLVRTKRDWLVKQRGWDGFVEFFHV

Sequence of entity 2 (E, F, G, H), FASTA

>9CPN_2 Bcl-2 homologous antagonist/killer (chains E, F, G, H)
SSTMGQVGRQLAIIGDDINRRY

Primary citation

Structural basis of BAK sequestration by MCL-1 in apoptosis. Srivastava, S., Sekar, G., Ojoawo, A. et al. Mol Cell (2025) 85:1606-1623.e10. DOI 10.1016/j.molcel.2025.03.013 · PubMed

Other PDB entries of the same protein (UniProt Q16611 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5VX1 1.22 Å, Bak L100A
8CZF 1.3 Å, Human BAK in complex with the dF2 peptide
8CZH 1.3 Å, Human BAK in complex with the dM2 peptide
2IMS 1.48 Å, The X-ray Structure of a Bak Homodimer Reveals an Inhibitory Zinc Binding Site
2IMT 1.49 Å, The X-ray Structure of a Bak Homodimer Reveals an Inhibitory Zinc Binding Site
9CPE 1.49 Å, Structural basis of BAK sequestration by MCL-1 and consequences for apoptosis initiation
5FMI 1.49 Å, Human Bak Q77L
7M5A 1.5 Å, Crystal Structure of human BAK in complex with W3W5_BID
5VWY 1.55 Å, Bak core latch dimer in complex with Bim-h3Pc-RT
5VX0 1.6 Å, Bak in complex with Bim-h3Glg
5VWZ 1.62 Å, Bak in complex with Bim-h3Pc
6UXQ 1.7 Å, Crystal structure of BAK core domain BH3-groove-dimer in complex with POPC and C8E4

Browse structure collections

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