8ZYO: Astemizole-bound hERG Channel

Cryo-EM Structure of astemizole-bound hERG Channel. Determined by electron microscopy at 3.29 Å resolution. Released 18 Sept 2024.

Method: Electron microscopy
Resolution: 3.29 Å
Organism: Homo sapiens
Chains: 4
Atoms: 6,238
Mol. weight: 367.63 kDa
Ligands: XB7
Released: 18 Sept 2024

Explore 8ZYO in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8ZYO contains 47 α-helices and 0 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: 14 helices, 0 β-strands

Element	Residues	Length
α-helix	410-431	22
α-helix	453-469	17
α-helix	490-494	5
α-helix	498-503	6
α-helix	521-524	4
α-helix	525-531	7
α-helix	532-537	6
α-helix	539-542	4
α-helix	546-574	29
α-helix	585-592	8
α-helix	607-623	17
α-helix	635-651	17
α-helix	652-656	5
α-helix	659-664	6

Chain B: 12 helices, 0 β-strands

Element	Residues	Length
α-helix	408-427	20
α-helix	428-432	5
α-helix	453-470	18
α-helix	499-504	6
α-helix	521-524	4
α-helix	525-529	5
α-helix	532-537	6
α-helix	539-542	4
α-helix	548-574	27
α-helix	585-592	8
α-helix	607-623	17
α-helix	635-662	28

Chain C: 9 helices, 0 β-strands

Element	Residues	Length
α-helix	408-431	24
α-helix	521-525	5
α-helix	526-532	7
α-helix	533-537	5
α-helix	538-540	3
α-helix	546-575	30
α-helix	586-593	8
α-helix	607-622	16
α-helix	635-664	30

Chain D: 12 helices, 0 β-strands

Element	Residues	Length
α-helix	408-430	23
α-helix	453-469	17
α-helix	490-493	4
α-helix	499-502	4
α-helix	522-525	4
α-helix	526-531	6
α-helix	532-537	6
α-helix	539-542	4
α-helix	546-574	29
α-helix	585-592	8
α-helix	607-622	16
α-helix	635-664	30

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Potassium voltage-gated channel subfamily H member 2	A, B, C, D	protein	820	Homo sapiens	Q12809 (AlphaFold model)

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

>8ZYO_1 Potassium voltage-gated channel subfamily H member 2 (chains A, B, C, D)
MPVRRGHVAPQNTFLDTIIRKFEGQSRKFIIANARVENCAVIYCNDGFCELCGYSRAEVM
QRPCTCDFLHGPRTQRRAAAQIAQALLGAEERKVEIAFYRKDGSCFLCLVDVVPVKNEDG
AVIMFILNFEVVMEKDMVGSSPTSDREIIAPKIKERTHNVTEKVTQVLSLGADVLPEYKL
QAPRIHRWTILHYSPFKAVWDWLILLLVIYTAVFTPYSAAFLLKETEEGPPATECGYACQ
PLAVVDLIVDIMFIVDILINFRTTYVNANEEVVSHPGRIAVHYFKGWFLIDMVAAIPFDL
LIFGSGSEELIGLLKTARLLRLVRVARKLDRYSEYGAAVLFLLMCTFALIAHWLACIWYA
IGNMEQPHMDSRIGWLHNLGDQIGKPYNSSGLGGPSIKDKYVTALYFTFSSLTSVGFGNV
SPNTNSEKIFSICVMLIGSLMYASIFGNVSAIIQRLYSGTARYHTQMLRVREFIRFHQIP
NPLRQRLEEYFQHAWSYTNGIDMNAVLKGFPECLQADICLHLNRSLLQHCKPFRGATKGC
LRALAMKFKTTHAPPGDTLVHAGDLLTALYFISRGSIEILRGDVVVAILGKNDIFGEPLN
LYARPGKSNGDVRALTYCDLHKIHRDDLLEVLDMYPEFSDHFWSSLEITFNLRDTNMIPG
GRQYQELPRCPAPTPSLLNIPLSSPGRRPRGDVESRLDALQRQLNRLETRLSADMATVLQ
LLQRQMTLVPPAYSAVTTPGPGPTSTSPLLPVSPLPTLTLDSLSQVSQFMACEELPPGAP
ELPQEGPTRRLSLPGQLGALTSQPLHRHGSDPGSLEVLFQ

Ligands and cofactors

ID	Name	Formula	Copies
XB7	1-[(4-fluorophenyl)methyl]-N-{1-[2-(4-methoxyphenyl)ethyl]piperidin-4-yl}-1H-be…	C28 H31 F N4 O	1

Primary citation

Improved higher resolution cryo-EM structures reveal the binding modes of hERG channel inhibitors. Miyashita, Y., Moriya, T., Kato, T. et al. Structure (2024) 32:1926. DOI 10.1016/j.str.2024.08.021 · PubMed

Other PDB entries of the same protein (UniProt Q12809 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4HQA 1.96 Å, Crystal structure of PAS domain from the human ERG (hERG) potassium channel
4HP9 2.12 Å, Crystal structure of the N-terminal truncated PAS domain from the hERG potassium channel
1BYW 2.6 Å, Structure of the N-terminal domain of the human-erg potassium channel
9CHQ 3.0 Å, Cryo-EM structure of the human ether-a-go-go related K+ channel (hERG) in 3 mM K+
8ZYQ 3.18 Å, Cryo-EM Structure of pimozide-bound hERG Channel
8ZYP 3.19 Å, Cryo-EM Structure of E-4031-bound hERG Channel
8ZYN 3.27 Å, Cryo-EM Structure of inhibitor-free hERG Channel
9CHP 3.3 Å, Cryo-EM structure of the human ether-a-go-go related K+ channel (hERG) in 300 mM K+
9CHS 3.4 Å, Cryo-EM structure of the human ether-a-go-go related K+ channel (hERG) in 3 mM K+…
8IO4 3.5 Å, Herg1a-herg1b open state
9CHR 3.5 Å, Cryo-EM structure of the human ether-a-go-go related K+ channel (hERG) in 300 mM K+…
5VA1 3.7 Å, Cryo-EM structure of the human ether-a-go-go related K+ channel

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