9BC6 | pdb_00009bc6

HCN1 M305L with propofol

PDB DOI: https://doi.org/10.2210/pdb9BC6/pdb
EM Map EMD-44425: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): Yes
Membrane Protein: Yes PDBTM MemProtMD

Deposited: 2024-04-07 Released: 2024-07-31
Deposition Author(s): Kim, E.D., Nimigean, C.M.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Propofol rescues voltage-dependent gating of HCN1 channel epilepsy mutants.

Kim, E.D., Wu, X., Lee, S., Tibbs, G.R., Cunningham, K.P., Di Zanni, E., Perez, M.E., Goldstein, P.A., Accardi, A., Larsson, H.P., Nimigean, C.M.

(2024) Nature 632: 451-459

PubMed: 39085604 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41586-024-07743-z
Primary Citation Related Structures:
8UC7, 8UC8, 9BC6, 9BC7

PubMed Abstract:
Hyperpolarization-activated cyclic nucleotide-gated (HCN) channels ¹ are essential for pacemaking activity and neural signalling ^2,3. Drugs inhibiting HCN1 are promising candidates for management of neuropathic pain ⁴ and epileptic seizures ⁵. The general anaesthetic propofol (2,6-di-iso-propylphenol) is a known HCN1 allosteric inhibitor ⁶ with unknown structural basis. Here, using single-particle cryo-electron microscopy and electrophysiology, we show that propofol inhibits HCN1 by binding to a mechanistic hotspot in a groove between the S5 and S6 transmembrane helices. We found that propofol restored voltage-dependent closing in two HCN1 epilepsy-associated polymorphisms that act by destabilizing the channel closed state: M305L, located in the propofol-binding site in S5, and D401H in S6 (refs. ^7,8). To understand the mechanism of propofol inhibition and restoration of voltage-gating, we tracked voltage-sensor movement in spHCN channels and found that propofol inhibition is independent of voltage-sensor conformational changes. Mutations at the homologous methionine in spHCN and an adjacent conserved phenylalanine in S6 similarly destabilize closing without disrupting voltage-sensor movements, indicating that voltage-dependent closure requires this interface intact. We propose a model for voltage-dependent gating in which propofol stabilizes coupling between the voltage sensor and pore at this conserved methionine-phenylalanine interface in HCN channels. These findings unlock potential exploitation of this site to design specific drugs targeting HCN channelopathies.

Organizational Affiliation

Department of Anesthesiology, Weill Cornell Medical College, New York, NY, USA.

Macromolecule Content

Total Structure Weight: 305.51 kDa
Atom Count: 14,972
Modeled Residue Count: 1,936
Deposited Residue Count: 2,640
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 1	A, B, C, D	660	Homo sapiens	Mutation(s): 1 Gene Names: HCN1, BCNG1 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for O60741 (Homo sapiens) Explore O60741 Go to UniProtKB: O60741
PHAROS: O60741 GTEx: ENSG00000164588
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O60741
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PCW Query on PCW Download:Ideal Coordinates CCD File SDF format, chain P [auth D] SDF format, chain O [auth D] SDF format, chain M [auth C] SDF format, chain L [auth C] SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain P [auth D] MOL2 format, chain O [auth D] MOL2 format, chain M [auth C] MOL2 format, chain L [auth C] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain P [auth D] mmCIF format, chain O [auth D] mmCIF format, chain M [auth C] mmCIF format, chain L [auth C] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] I [auth B] J [auth B] L [auth C] E [auth A], F [auth A], I [auth B], J [auth B], L [auth C], M [auth C], O [auth D], P [auth D]	1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE C₄₄ H₈₅ N O₈ P SNKAWJBJQDLSFF-NVKMUCNASA-O		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain O [auth D] Focus chain P [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain O [auth D] Focus chain P [auth D]
PFL (Subject of Investigation/LOI) Query on PFL Download:Ideal Coordinates CCD File SDF format, chain N [auth D] SDF format, chain K [auth C] SDF format, chain H [auth B] SDF format, chain G [auth A] MOL2 format, chain N [auth D] MOL2 format, chain K [auth C] MOL2 format, chain H [auth B] MOL2 format, chain G [auth A] mmCIF format, chain N [auth D] mmCIF format, chain K [auth C] mmCIF format, chain H [auth B] mmCIF format, chain G [auth A]	G [auth A], H [auth B], K [auth C], N [auth D]	2,6-BIS(1-METHYLETHYL)PHENOL C₁₂ H₁₈ O OLBCVFGFOZPWHH-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain N [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain N [auth D]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21rc1_5109:

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2024-07-31

Deposition Author(s):

Kim, E.D.

Nimigean, C.M.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM124451
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	United States	NS137561