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- PDB-8io3: Cryo-EM structure of human HCN3 channel with cilobradine -

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Basic information

Entry
Database: PDB / ID: 8io3
TitleCryo-EM structure of human HCN3 channel with cilobradine
ComponentsPotassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 3
KeywordsMEMBRANE PROTEIN / human HCN3 channel
Function / homology
Function and homology information


HCN channels / HCN channel complex / regulation of SA node cell action potential / regulation of membrane depolarization / sodium ion import across plasma membrane / voltage-gated sodium channel activity / potassium ion import across plasma membrane / regulation of heart rate by cardiac conduction / voltage-gated potassium channel activity / cAMP binding ...HCN channels / HCN channel complex / regulation of SA node cell action potential / regulation of membrane depolarization / sodium ion import across plasma membrane / voltage-gated sodium channel activity / potassium ion import across plasma membrane / regulation of heart rate by cardiac conduction / voltage-gated potassium channel activity / cAMP binding / potassium ion transmembrane transport / sodium ion transmembrane transport / cellular response to cAMP / regulation of membrane potential / axon / dendrite / plasma membrane
Similarity search - Function
Ion transport N-terminal / Ion transport protein N-terminal / : / Potassium channel, voltage-dependent, EAG/ELK/ERG / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / RmlC-like jelly roll fold ...Ion transport N-terminal / Ion transport protein N-terminal / : / Potassium channel, voltage-dependent, EAG/ELK/ERG / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / RmlC-like jelly roll fold / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
: / Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.02 Å
AuthorsYu, B. / Lu, Q.Y. / Li, J. / Zhang, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure of human HCN3 channel with cilobradine
Authors: Yu, B. / Lu, Q.Y. / Li, J. / Zhang, J.
History
DepositionMar 10, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 10, 2024Provider: repository / Type: Initial release
Revision 1.0Apr 10, 2024Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 10, 2024Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 10, 2024Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 10, 2024Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 10, 2024Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jun 25, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details
Item: _em_admin.last_update / _em_software.name / _pdbx_entry_details.has_protein_modification
Revision 1.1Jun 25, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 3
A: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 3
B: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 3
D: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)346,5028
Polymers344,5724
Non-polymers1,9304
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 3


Mass: 86142.922 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HCN3, KIAA1535
Production host: Mammalian expression vector EGFP-MCS-pcDNA3.1 (others)
References: UniProt: Q9P1Z3
#2: Chemical
ChemComp-VXI / 3-[[(3~{S})-1-[2-(3,4-dimethoxyphenyl)ethyl]piperidin-3-yl]methyl]-7,8-dimethoxy-2,5-dihydro-1~{H}-3-benzazepin-4-one / Cilobradine


Mass: 482.612 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C28H38N2O5 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: otassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 3
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Mammalian expression vector BsrGI-MCS-pcDNA3.1 (others)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1800 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.02 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 121387 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00613992
ELECTRON MICROSCOPYf_angle_d0.88619036
ELECTRON MICROSCOPYf_dihedral_angle_d9.2728016
ELECTRON MICROSCOPYf_chiral_restr0.0522156
ELECTRON MICROSCOPYf_plane_restr0.0062340

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