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- PDB-9r1v: Structure of the human chimera HCN112 hyperpolarization-activated... -

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Basic information

Entry
Database: PDB / ID: 9r1v
TitleStructure of the human chimera HCN112 hyperpolarization-activated cyclic nucleotide-gated ion channel.
ComponentsPotassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 1,Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2
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 / cellular response to aldosterone / HCN channel complex / retinal cone cell development / ammonium transmembrane transport / cellular response to cGMP / intracellularly cAMP-activated cation channel activity ...: / positive regulation of membrane hyperpolarization / HCN channels / general adaptation syndrome, behavioral process / cellular response to aldosterone / HCN channel complex / retinal cone cell development / ammonium transmembrane transport / cellular response to cGMP / intracellularly cAMP-activated cation channel activity / negative regulation of action potential / regulation of SA node cell action potential / membrane depolarization during cardiac muscle 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 / voltage-gated potassium channel complex / presynaptic active zone membrane / potassium ion transmembrane transport / dendrite membrane / axon terminus / cellular response to cAMP / dendritic shaft / sodium ion transmembrane transport / PDZ domain binding / regulation of membrane potential / response to calcium ion / cell-cell signaling / protein homotetramerization / molecular adaptor activity / basolateral plasma membrane / postsynaptic membrane / response to xenobiotic stimulus / axon / neuronal cell body / dendrite / protein-containing complex binding / 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 / Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.53 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: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 1,Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2
B: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 1,Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2
C: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 1,Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2
D: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 1,Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2


Theoretical massNumber of molelcules
Total (without water)296,3964
Polymers296,3964
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, Tetramer, gel filtration, Tetramer, scanning transmission electron microscopy, Tetramer
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 1,Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2 / Brain cyclic nucleotide-gated channel 1 / BCNG-1 / Brain cyclic nucleotide-gated channel 2 / BCNG-2


Mass: 74099.016 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HCN1, BCNG1, HCN2, BCNG2 / Cell line (production host): HEK293S GnTI- / Production host: Homo sapiens (human) / References: UniProt: O60741, UniProt: Q9UL51
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
Type: COMPLEX / Details: HCN112 Chimera between HCN1 and HCN2 / 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
Specimen supportGrid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: UltrAuFoil R2/2
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 recordingAverage exposure time: 6.25 sec. / Electron dose: 41.42 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of real images: 5042

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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
14PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 370859
SymmetryPoint symmetry: C4 (4 fold cyclic)
3D reconstructionResolution: 3.53 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 92412 / 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_d0.00315044
ELECTRON MICROSCOPYf_angle_d0.61620428
ELECTRON MICROSCOPYf_dihedral_angle_d4.8512052
ELECTRON MICROSCOPYf_chiral_restr0.0412272
ELECTRON MICROSCOPYf_plane_restr0.0042576

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