9JO3: Human BKca channel-compound 10b complex

Cryo-EM structure of human BKca channel-compound 10b complex. Determined by electron microscopy at 2.8 Å resolution. Released 26 Feb 2025.

Method: Electron microscopy
Resolution: 2.8 Å
Organism: Homo sapiens
Chains: 4
Atoms: 29,981
Mol. weight: 513.89 kDa
Ligands: MG, CA, A1L4E, Y01
Released: 26 Feb 2025

Explore 9JO3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9JO3 contains 199 α-helices and 125 β-strands across 4 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: 48 helices, 31 β-strands

Element	Residues	Length	Sheet
α-helix	22-50	29
α-helix	93-105	13
α-helix	110-133	24
β-strand	139-141	3	1
α-helix	144-146	3
α-helix	152-170	19
α-helix	174-178	5
α-helix	181-199	19
β-strand	201-203	3	1
α-helix	207-215	9
α-helix	216-222	7
α-helix	230-258	29
α-helix	262-264	3
α-helix	274-285	12
α-helix	298-325	28
β-strand	344-348	5	2
α-helix	353-363	11
α-helix	369-370	2
β-strand	374-379	6	2
α-helix	385-393	9
β-strand	398-402	5	2
α-helix	408-413	6
β-strand	421-424	4	2
α-helix	433-450	18
β-strand	455-460	6	2
α-helix	464-466	3
α-helix	467-470	4
β-strand	482-485	4	2
α-helix	486-499	14
α-helix	503-507	5
α-helix	524-531	8
β-strand	535-540	6	3
α-helix	543-545	3
β-strand	549	1	4
α-helix	550-556	7
α-helix	557-561	5
β-strand	564-570	7	3
β-strand	576-578	3	3
β-strand	587	1	4
β-strand	594-599	6	3
α-helix	602-605	4
α-helix	607-610	4
α-helix	613-616	4
β-strand	744	1	5
β-strand	745	1	6
β-strand	750	1	7
β-strand	751	1	5
α-helix	758-760	3
β-strand	762	1	8
α-helix	765-770	6
β-strand	776-781	6	8
α-helix	793-796	4
α-helix	798-800	3
β-strand	801	1	7
α-helix	809-811	3
β-strand	812-816	5	8
α-helix	818-821	4
α-helix	825-827	3
β-strand	834-838	5	8
α-helix	846-849	4
β-strand	855-861	7	8
α-helix	876-886	11
α-helix	931-933	3
β-strand	937-940	4	8
α-helix	943-949	7
α-helix	965-968	4
β-strand	972-974	3	8
α-helix	975-980	6
α-helix	981-987	7
α-helix	991-994	4
α-helix	1005-1013	9
β-strand	1019	1	6
α-helix	1024-1027	4
β-strand	1034-1039	6	9
α-helix	1048-1051	4
α-helix	1054-1065	12
β-strand	1068-1075	8	9
β-strand	1089-1093	5	9
β-strand	1105-1111	7	9

Chain B: 53 helices, 33 β-strands

Element	Residues	Length	Sheet
α-helix	22-51	30
α-helix	93-105	13
α-helix	110-134	25
β-strand	139-141	3	10
α-helix	152-170	19
α-helix	174-178	5
α-helix	181-199	19
β-strand	201-203	3	10
α-helix	207-215	9
α-helix	216-223	8
α-helix	230-258	29
α-helix	262-264	3
α-helix	274-285	12
α-helix	298-325	28
β-strand	344-348	5	11
α-helix	353-363	11
α-helix	369-370	2
β-strand	374-379	6	11
α-helix	385-393	9
β-strand	398-402	5	11
α-helix	408-413	6
α-helix	416-418	3
β-strand	422-424	3	11
α-helix	433-450	18
β-strand	456-460	5	11
α-helix	463-466	4
α-helix	467-471	5
β-strand	482-485	4	11
α-helix	486-499	14
α-helix	503-508	6
α-helix	524-532	9
β-strand	535-540	6	12
α-helix	541-542	2
α-helix	543-545	3
β-strand	549	1	13
α-helix	550-556	7
α-helix	557-561	5
β-strand	564-568	5	12
β-strand	580-581	2	12
β-strand	588	1	13
β-strand	594-599	6	12
α-helix	606-609	4
α-helix	613-616	4
β-strand	744	1	14
β-strand	745	1	15
β-strand	750	1	16
β-strand	751	1	14
α-helix	758-761	4
β-strand	762	1	17
α-helix	765-770	6
β-strand	777-782	6	17
α-helix	788-789	2
α-helix	793-796	4
α-helix	797-800	4
β-strand	801	1	16
α-helix	806-808	3
α-helix	809-811	3
β-strand	812-816	5	17
α-helix	818-822	5
α-helix	825-827	3
β-strand	834-838	5	17
α-helix	844-849	6
α-helix	852-854	3
β-strand	857-862	6	17
α-helix	876-886	11
β-strand	889	1	18
β-strand	930	1	18
β-strand	936-940	5	17
α-helix	943-948	6
α-helix	961-963	3
α-helix	965-968	4
β-strand	972-974	3	17
α-helix	975-978	4
α-helix	981-987	7
α-helix	991-996	6
α-helix	997-1001	5
α-helix	1005-1013	9
β-strand	1019	1	15
α-helix	1024-1027	4
α-helix	1028-1030	3
β-strand	1033-1038	6	19
α-helix	1046-1049	4
α-helix	1054-1065	12
β-strand	1068-1075	8	19
β-strand	1089-1093	5	19
β-strand	1105-1112	8	19

Chain C: 50 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	22-30	9
α-helix	31-35	5
α-helix	36-51	16
α-helix	93-105	13
α-helix	110-133	24
α-helix	152-170	19
α-helix	174-178	5
α-helix	181-199	19
α-helix	206-216	11
α-helix	217-223	7
α-helix	230-259	30
α-helix	262-264	3
α-helix	274-285	12
α-helix	298-325	28
β-strand	344-349	6	20
α-helix	353-363	11
β-strand	374-379	6	20
α-helix	385-393	9
β-strand	398-402	5	20
α-helix	408-413	6
α-helix	416-418	3
β-strand	421-425	5	20
α-helix	433-450	18
β-strand	456-460	5	20
α-helix	464-471	8
β-strand	482-485	4	20
α-helix	486-499	14
α-helix	503-507	5
α-helix	524-532	9
β-strand	535-540	6	21
α-helix	541-542	2
α-helix	543-545	3
β-strand	549	1	22
α-helix	550-554	5
α-helix	558-561	4
β-strand	564-570	7	21
α-helix	571-573	3
β-strand	578-581	4	21
β-strand	588	1	22
β-strand	594-599	6	21
α-helix	602-610	9
α-helix	613-616	4
β-strand	744-745	2	23
β-strand	750	1	24
β-strand	751	1	23
α-helix	758-761	4
β-strand	762	1	25
α-helix	765-770	6
β-strand	777-782	6	25
α-helix	788-790	3
α-helix	793-796	4
α-helix	798-800	3
β-strand	801	1	24
α-helix	806-808	3
α-helix	809-811	3
β-strand	812-816	5	25
α-helix	818-824	7
β-strand	834-838	5	25
α-helix	844-849	6
β-strand	857-862	6	25
α-helix	876-887	12
β-strand	937-939	3	25
α-helix	943-949	7
α-helix	961-963	3
α-helix	965-968	4
β-strand	972-973	2	25
α-helix	975-978	4
α-helix	981-987	7
α-helix	991-1000	10
α-helix	1005-1014	10
β-strand	1019-1020	2	23
α-helix	1026-1028	3
β-strand	1034-1039	6	26
α-helix	1047-1049	3
α-helix	1054-1065	12
β-strand	1068-1075	8	26
β-strand	1089-1093	5	26
β-strand	1105-1111	7	26

Chain D: 48 helices, 33 β-strands

Element	Residues	Length	Sheet
α-helix	22-51	30
α-helix	93-105	13
α-helix	110-133	24
β-strand	139-141	3	27
α-helix	152-170	19
α-helix	174-178	5
α-helix	181-189	9
α-helix	191-199	9
β-strand	201-203	3	27
α-helix	207-216	10
α-helix	217-223	7
α-helix	232-258	27
α-helix	262-264	3
α-helix	274-285	12
α-helix	298-325	28
β-strand	344-349	6	28
α-helix	353-363	11
α-helix	369-370	2
β-strand	374-379	6	28
α-helix	385-393	9
β-strand	398-402	5	28
α-helix	408-413	6
β-strand	422-425	4	28
α-helix	433-450	18
β-strand	456-460	5	28
α-helix	463-469	7
β-strand	482-485	4	28
α-helix	486-499	14
α-helix	503-508	6
α-helix	524-531	8
β-strand	535-540	6	29
α-helix	541-542	2
α-helix	543-545	3
β-strand	549	1	30
α-helix	550-554	5
β-strand	564-568	5	29
β-strand	580-581	2	29
β-strand	588	1	30
β-strand	594-599	6	29
α-helix	602-605	4
β-strand	744	1	31
β-strand	745	1	32
β-strand	750	1	33
β-strand	751	1	31
α-helix	758-761	4
β-strand	762	1	34
α-helix	765-770	6
β-strand	777-782	6	34
α-helix	788-789	2
α-helix	793-796	4
β-strand	801	1	33
α-helix	806-808	3
α-helix	809-811	3
β-strand	812-816	5	34
α-helix	818-821	4
α-helix	825-827	3
β-strand	834-838	5	34
α-helix	844-849	6
α-helix	852-854	3
β-strand	857-862	6	34
α-helix	871-873	3
α-helix	876-886	11
β-strand	889	1	35
β-strand	930	1	35
β-strand	936-940	5	34
α-helix	943-948	6
α-helix	961-963	3
α-helix	965-968	4
β-strand	972-974	3	34
α-helix	975-978	4
α-helix	981-987	7
α-helix	991-999	9
α-helix	1005-1014	10
β-strand	1019	1	32
α-helix	1027-1030	4
β-strand	1034-1039	6	36
α-helix	1047-1051	5
α-helix	1054-1065	12
β-strand	1068-1075	8	36
β-strand	1089-1093	5	36
β-strand	1105-1111	7	36

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Calcium-activated potassium channel subunit alpha-1	A, B, C, D	protein	1119	Homo sapiens	Q12791 (AlphaFold model)

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

>9JO3_1 Calcium-activated potassium channel subunit alpha-1 (chains A, B, C, D)
MDALIIPVTMEVPCDSRGQRMWWAFLASSMVTFFGGLFIILLWRTLKYLWTVCCHCGGKT
KEAQKINNGSSQADGTLKPVDEKEEAVAAEVGWMTSVKDWAGVMISAQTLTGRVLVVLVF
ALSIGALVIYFIDSSNPIESCQNFYKDFTLQIDMAFNVFFLLYFGLRFIAANDKLWFWLE
VNSVVDFFTVPPVFVSVYLNRSWLGLRFLRALRLIQFSEILQFLNILKTSNSIKLVNLLS
IFISTWLTAAGFIHLVENSGDPWENFQNNQALTYWECVYLLMVTMSTVGYGDVYAKTTLG
RLFMVFFILGGLAMFASYVPEIIELIGNRKKYGGSYSAVSGRKHIVVCGHITLESVSNFL
KDFLHKDRDDVNVEIVFLHNISPNLELEALFKRHFTQVEFYQGSVLNPHDLARVKIESAD
ACLILANKYCADPDAEDASNIMRVISIKNYHPKIRIITQMLQYHNKAHLLNIPSWNWKEG
DDAICLAELKLGFIAQSCLAQGLSTMLANLFSMRSFIKIEEDTWQKYYLEGVSNEMYTEY
LSSAFVGLSFPTVCELCFVKLKLLMIAIEYKSANRESRILINPGNHLKIQEGTLGFFIAS
DAKEVKRAFFYCKACHDDITDPKRIKKCGCKRPKMSIYKRMRRACCFDCGRSERDCSCMS
GRVRGNVDTLERAFPLSSVSVNDCSTSFRAFEDEQPSTLSPKKKQRNGGMRNSPNTSPKL
MRHDPLLIPGNDQIDNMDSNVKKYDSTGMFHWCAPKEIEKVILTRSEAAMTVLSGHVVVC
IFGDVSSALIGLRNLVMPLRASNFHYHELKHIVFVGSIEYLKREWETLHNFPKVSILPGT
PLSRADLRAVNINLCDMCVILSANQNNIDDTSLQDKECILASLNIKSMQFDDSIGVLQAN
SQGFTPPGMDRSSPDNSPVHGMLRQPSITTGVNIPIITELVNDTNVQFLDQDDDDDPDTE
LYLTQPFACGTAFAVSVLDSLMSATYFNDNILTLIRTLVTGGATPELEALIAEENALRGG
YSTPQTLANRDRCRVAQLALLDGPFADLGDGGCYGDLFCKALKTYNMLCFGIYRLRDAHL
STPSQCTKRYVITNPPYEFELVPTDLIFCLMQFDHNAGQ

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	4
CA	Calcium ion	Ca	8
A1L4E	5-azanyl-2-[2,3,5,6-tetrakis(fluoranyl)-4-(trifluoromethyl)phenoxy]phenol	C13 H6 F7 N O2	4
Y01	Cholesterol hemisuccinate	C31 H50 O4	16

Water and common crystallization additives (K) are not listed.

Primary citation

Discovery of Diphenyl Ether Derivatives as Novel BK Ca Channel Activators: Structure-Activity Relationship, Cryo-EM Complex Structures, and In Vivo Animal Studies. Park, S.B., Lee, N.Y., Lee, E.Y. et al. J Med Chem (2025) 68:4259-4286. DOI 10.1021/acs.jmedchem.4c02008 · PubMed

Other PDB entries of the same protein (UniProt Q12791 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6V5A 2.0 Å, Crystal structure of the human BK channel gating ring L390P mutant
8V60 2.43 Å, F315A mutant of human Slo1 in presence of EDTA - resting VSD
11DA 2.57 Å, Human Slo1-PenitremA complex under divalent chelated condition - full model
9CZM 2.57 Å, Ca2+ bound open-inactivated hSlo1 + beta2N-beta4 channel in nanodisc.
11DC 2.58 Å, Human Slo1-PenitremA complex under divalent chelated condition - gating-ring masked out
11CZ 2.6 Å, Human Slo1-paxilline complex under divalent chelated condition - full model
8V64 2.6 Å, RCK1-RCK2 double mutant of human Slo1 in presence of EDTA - resting VSD
8GHF 2.7 Å, cryo-EM structure of hSlo1 in plasma membrane vesicles
11DB 2.71 Å, Human Slo1-Paxilline complex under divalent chelated condition - gating-ring masked
8V63 2.72 Å, R207A mutant of human Slo1 in presence of EDTA - activated VSD
8VAZ 2.82 Å, Structure of human Slo1 and human LRRC26 in EDTA - LRRD masked
9CZO 2.87 Å, Ca2+ bound intermediate state of hSlo1 + beta2N-beta4 channel in nanodisc.

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