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- PDB-9r1u: Structure of the human HCN1dC hyperpolarization-activated cyclic ... -

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Basic information

Entry
Database: PDB / ID: 9r1u
TitleStructure of the human HCN1dC hyperpolarization-activated cyclic nucleotide-gated ion channel.
ComponentsPotassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 1
KeywordsMEMBRANE PROTEIN / Ion channel / HCN channel / pacemaker channel
Function / homology
Function and homology information


: / positive regulation of membrane hyperpolarization / HCN channels / general adaptation syndrome, behavioral process / HCN channel complex / retinal cone cell development / intracellularly cAMP-activated cation channel activity / negative regulation of action potential / regulation of SA node cell action potential / maternal behavior ...: / positive regulation of membrane hyperpolarization / HCN channels / general adaptation syndrome, behavioral process / HCN channel complex / retinal cone cell development / intracellularly cAMP-activated cation channel activity / negative regulation of action potential / regulation of SA node cell action potential / maternal behavior / apical dendrite / sodium ion import across plasma membrane / apical protein localization / response to L-glutamate / negative regulation of synaptic transmission, glutamatergic / voltage-gated sodium channel activity / voltage-gated monoatomic cation channel activity / regulation of membrane depolarization / potassium ion import across plasma membrane / phosphatidylinositol-3,4,5-trisphosphate binding / regulation of heart rate by cardiac conduction / voltage-gated potassium channel activity / potassium channel activity / cAMP binding / neuronal action potential / cellular response to interferon-beta / phosphatidylinositol-4,5-bisphosphate binding / presynaptic active zone membrane / potassium ion transmembrane transport / dendrite membrane / axon terminus / cellular response to cAMP / dendritic shaft / sodium ion transmembrane transport / regulation of membrane potential / response to calcium ion / protein homotetramerization / basolateral plasma membrane / postsynaptic membrane / axon / neuronal cell body / dendrite / glutamatergic synapse / cell surface / identical protein binding / plasma membrane
Similarity search - Function
Ion transport N-terminal / Ion transport protein N-terminal / : / Potassium channel, voltage-dependent, EAG/ELK/ERG / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain ...Ion transport N-terminal / Ion transport protein N-terminal / : / Potassium channel, voltage-dependent, EAG/ELK/ERG / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / 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 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.92 Å
AuthorsZorzini, V. / Ulens, C.
Funding support Belgium, 2items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)12W4618N Belgium
Research Foundation - Flanders (FWO) Belgium
CitationJournal: To Be Published
Title: Interactions between CNBD and HCND domains control gating inhibition in HCN1 family.
Authors: Zorzini, V. / Gallardo, R. / Brams, M. / Ulens, C.
History
DepositionApr 28, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 2026Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 1
B: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 1
C: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 1
D: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 1


Theoretical massNumber of molelcules
Total (without water)177,6014
Polymers177,6014
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, Homotetramer, gel filtration, Homotetramer, scanning transmission electron microscopy, Homotetramer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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


Mass: 44400.227 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HCN1, BCNG1 / Cell line (production host): HEK293S GnTI- / Production host: Homo sapiens (human) / References: UniProt: O60741
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: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 1 delta C-terminus
Type: ORGANELLE OR CELLULAR COMPONENT / Details: HCN1dC / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293S GnTI-
Buffer solutionpH: 8
SpecimenConc.: 3.7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 278 K

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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: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3200 nm / Nominal defocus min: 1600 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 39.81 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
2EPUimage acquisition
4RELION3.1.2CTF correction
7UCSF Chimera1.15model fitting
9Coot0.8.9.2model refinement
12cryoSPARC3.2classification
13cryoSPARC3.23D reconstruction
20PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 370859
SymmetryPoint symmetry: C4 (4 fold cyclic)
3D reconstructionResolution: 3.92 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 20854 / Symmetry type: POINT
Atomic model buildingSpace: REAL
Atomic model buildingPDB-ID: 5U6O

5u6o


Accession code: 5U6O / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0039022
ELECTRON MICROSCOPYf_angle_d0.77912307
ELECTRON MICROSCOPYf_dihedral_angle_d7.6151258
ELECTRON MICROSCOPYf_chiral_restr0.0451424
ELECTRON MICROSCOPYf_plane_restr0.0031529

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