9D19: PDB entry 9D19

Ca2+ bound open-inactivated hSlo1 + beta2N-beta4 channel in detergent-conformation 3 of inactivating domain. Determined by electron microscopy at 2.88 Å resolution. Released 5 Mar 2025.

Method: Electron microscopy
Resolution: 2.88 Å
Organism: Homo sapiens
Chains: 8
Atoms: 36,018
Mol. weight: 605.63 kDa
Ligands: CLR, POV, CA, MG
Released: 5 Mar 2025

Explore 9D19 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9D19 contains 221 α-helices and 164 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.

Chains A, B, C and D: 51 helices, 35 β-strands

Element	Residues	Length	Sheet
α-helix	22-53	32
α-helix	93-105	13
α-helix	110-133	24
β-strand	139-141	3	1
α-helix	144-146	3
α-helix	148-170	23
α-helix	174-178	5
α-helix	181-189	9
α-helix	191-199	9
β-strand	201-203	3	1
α-helix	207-216	10
α-helix	217-223	7
α-helix	230-258	29
α-helix	262-264	3
α-helix	274-285	12
α-helix	298-325	28
β-strand	344-349	6	2
α-helix	353-363	11
β-strand	374-379	6	2
α-helix	382-384	3
α-helix	385-393	9
β-strand	398-402	5	2
α-helix	408-413	6
β-strand	422-425	4	2
α-helix	433-450	18
β-strand	456-460	5	2
α-helix	464-469	6
β-strand	482-485	4	2
α-helix	486-499	14
α-helix	503-509	7
α-helix	524-532	9
β-strand	535-536	2	3
β-strand	539-540	2	3
α-helix	543-545	3
β-strand	549	1	4
α-helix	550-556	7
α-helix	557-561	5
β-strand	564-568	5	3
β-strand	580-581	2	3
α-helix	587	1
β-strand	588	1	4
α-helix	589-590	2
β-strand	594-599	6	3
α-helix	602-609	8
β-strand	686-687	2	5
β-strand	692	1	6
β-strand	693	1	5
α-helix	700-703	4
β-strand	704	1	7
α-helix	707-712	6
β-strand	719-724	6	7
α-helix	730-731	2
α-helix	735-741	7
β-strand	743	1	6
α-helix	748-750	3
β-strand	754-757	4	7
α-helix	760-763	4
α-helix	767-769	3
β-strand	776-779	4	7
α-helix	786-791	6
α-helix	794-796	3
β-strand	799-804	6	7
α-helix	818-828	11
β-strand	831	1	8
β-strand	872	1	8
α-helix	873-875	3
β-strand	878-882	5	7
α-helix	885-890	6
α-helix	903-905	3
α-helix	907-910	4
β-strand	914-916	3	7
α-helix	917-920	4
α-helix	923-929	7
α-helix	931-942	12
α-helix	947-956	10
β-strand	961-962	2	5
α-helix	966-970	5
β-strand	976-981	6	9
β-strand	995	1	10
α-helix	996-1007	12
β-strand	1010-1017	8	9
β-strand	1031-1035	5	9
α-helix	1041	1
β-strand	1042	1	10
α-helix	1043	1
β-strand	1048-1053	6	9

Chain E: 5 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	8-10	3
α-helix	40-77	38
β-strand	80-83	4	41
β-strand	85-100	16	41
β-strand	108-120	13	41
β-strand	128-131	4	41
α-helix	134-139	6
α-helix	153-168	16
β-strand	177-181	5	41
β-strand	185-190	6	41
α-helix	197-233	37

Chains F, G and H: 4 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	40-77	38
β-strand	80-83	4	42
β-strand	85-100	16	42
β-strand	108-120	13	42
β-strand	128-131	4	42
α-helix	134-139	6
α-helix	153-168	16
β-strand	177-181	5	42
β-strand	185-190	6	42
α-helix	197-233	37

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Isoform 5 of Calcium-activated potassium channel subunit alpha-1	A, B, C, D	protein	1056	Homo sapiens	Q12791 (AlphaFold model)
Large-conductance Ca2+-activated K+ channel beta2 subunit,Calcium-activated potassium channel…	E, F, G, H	protein	239	Homo sapiens	B5BNX0 (AlphaFold model), Q86W47 (AlphaFold model)

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

>9D19_1 Isoform 5 of Calcium-activated potassium channel subunit alpha-1 (chains A, B, C, D)
MDALIIPVTMEVPCDSRGQRMWWAFLASSMVTFFGGLFIILLWRTLKYLWTVCCHCGGKT
KEAQKINNGSSQADGTLKPVDEKEEAVAAEVGWMTSVKDWAGVMISAQTLTGRVLVVLVF
ALSIGALVIYFIDSSNPIESCQNFYKDFTLQIDMAFNVFFLLYFGLRFIAANDKLWFWLE
VNSVVDFFTVPPVFVSVYLNRSWLGLRFLRALRLIQFSEILQFLNILKTSNSIKLVNLLS
IFISTWLTAAGFIHLVENSGDPWENFQNNQALTYWECVYLLMVTMSTVGYGDVYAKTTLG
RLFMVFFILGGLAMFASYVPEIIELIGNRKKYGGSYSAVSGRKHIVVCGHITLESVSNFL
KDFLHKDRDDVNVEIVFLHNISPNLELEALFKRHFTQVEFYQGSVLNPHDLARVKIESAD
ACLILANKYCADPDAEDASNIMRVISIKNYHPKIRIITQMLQYHNKAHLLNIPSWNWKEG
DDAICLAELKLGFIAQSCLAQGLSTMLANLFSMRSFIKIEEDTWQKYYLEGVSNEMYTEY
LSSAFVGLSFPTVCELCFVKLKLLMIAIEYKSANRESRILINPGNHLKIQEGTLGFFIAS
DAKEVKRAFFYCKACHDDITDPKRIKKCGCKRLEDEQPSTLSPKKKQRNGGMRNSPNTSP
KLMRHDPLLIPGNDQIDNMDSNVKKYDSTGMFHWCAPKEIEKVILTRSEAAMTVLSGHVV
VCIFGDVSSALIGLRNLVMPLRASNFHYHELKHIVFVGSIEYLKREWETLHNFPKVSILP
GTPLSRADLRAVNINLCDMCVILSANQNNIDDTSLQDKECILASLNIKSMQFDDSIGVLQ
ANSQGFTPPGMDRSSPDNSPVHGMLRQPSITTGVNIPIITELVNDTNVQFLDQDDDDDPD
TELYLTQPFACGTAFAVSVLDSLMSATYFNDNILTLIRTLVTGGATPELEALIAEENALR
GGYSTPQTLANRDRCRVAQLALLDGPFADLGDGGCYGDLFCKALKTYNMLCFGIYRLRDA
HLSTPSQCTKRYVITNPPYEFELVPTDLIFCLMQFD

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

>9D19_2 Large-conductance Ca2+-activated K+ channel beta2 subunit,Calcium-activated potassium channel subunit beta-4 (chains E, F, G, H)
FIWTSGRTSSSYRHDEKRNIYQKIRDHDLLDKRKTVTALKAGEDKSIRLGLFLIISGVVS
LFIFGFCWLSPALQDLQATEANCTVLSVQQIGEVFECTFTCGADCRGTSQYPCVQVYVNN
SESNSRALLHSDEHQLLTNPKCSYIPPCKRENQKNLESVMNWQQYWKDEIGSQPFTCYFN
QHQRPDDVLLHRTHDEIVLLHCFLWPLVTFVVGVLIVVLTICAKSLAVKAEAMKKRKFS

Ligands and cofactors

ID	Name	Formula	Copies
CLR	Cholesterol	C27 H46 O	11
POV	(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl…	C42 H82 N O8 P	20
CA	Calcium ion	Ca	8
MG	Magnesium ion	Mg	4

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

Primary citation

Ball-and-chain inactivation of a human large conductance calcium-activated potassium channel. Agarwal, S., Kim, E.D., Lee, S. et al. Nat Commun (2025) 16:1769-1769. DOI 10.1038/s41467-025-56844-4 · 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
9JO3 2.8 Å, Cryo-EM structure of human BKca channel-compound 10b complex
8VAZ 2.82 Å, Structure of human Slo1 and human LRRC26 in EDTA - LRRD masked

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