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- EMDB-35606: Cryo-EM structure of human HCN3 channel with cilobradine -

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Basic information

Entry
Database: EMDB / ID: EMD-35606
TitleCryo-EM structure of human HCN3 channel with cilobradine
Map data
Sample
  • Complex: otassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 3
    • Protein or peptide: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 3
  • Ligand: 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
Keywordshuman HCN3 channel / MEMBRANE PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.02 Å
AuthorsYu B / Lu QY / Li J / Zhang J
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure of human HCN3 channel with cilobradine
Authors: Yu B / Lu QY / Li J / Zhang J
History
DepositionMar 10, 2023-
Header (metadata) releaseApr 10, 2024-
Map releaseApr 10, 2024-
UpdateJun 25, 2025-
Current statusJun 25, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35606.png

Downloads & links

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Map

FileDownload / File: emd_35606.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.53 Å/pix.
x 400 pix.
= 210.4 Å		0.53 Å/pix.
x 400 pix.
= 210.4 Å		0.53 Å/pix.
x 400 pix.
= 210.4 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.526 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.035
Minimum - Maximum-0.02984527 - 0.111165665
Average (Standard dev.)0.0049785757 (±0.008687585)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 210.40001 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_35606_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_35606_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : otassium/sodium hyperpolarization-activated cyclic nucleotide-gat...

EntireName: otassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 3
Components
  • Complex: otassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 3
    • Protein or peptide: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 3
  • Ligand: 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

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Supramolecule #1: otassium/sodium hyperpolarization-activated cyclic nucleotide-gat...

SupramoleculeName: otassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 3
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Potassium/sodium hyperpolarization-activated cyclic nucleotide-ga...

MacromoleculeName: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 3
type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 86.142922 KDa
Recombinant expressionOrganism: Mammalian expression vector EGFP-MCS-pcDNA3.1 (others)
SequenceString: MEAEQRPAAG ASEGATPGLE AVPPVAPPPA TAASGPIPKS GPEPKRRHLG TLLQPTVNKF SLRVFGSHKA VEIEQERVKS AGAWIIHPY SDFRFYWDLI MLLLMVGNLI VLPVGITFFK EENSPPWIVF NVLSDTFFLL DLVLNFRTGI VVEEGAEILL A PRAIRTRY ...String:
MEAEQRPAAG ASEGATPGLE AVPPVAPPPA TAASGPIPKS GPEPKRRHLG TLLQPTVNKF SLRVFGSHKA VEIEQERVKS AGAWIIHPY SDFRFYWDLI MLLLMVGNLI VLPVGITFFK EENSPPWIVF NVLSDTFFLL DLVLNFRTGI VVEEGAEILL A PRAIRTRY LRTWFLVDLI SSIPVDYIFL VVELEPRLDA EVYKTARALR IVRFTKILSL LRLLRLSRLI RYIHQWEEIF HM TYDLASA VVRIFNLIGM MLLLCHWDGC LQFLVPMLQD FPPDCWVSIN HMVNHSWGRQ YSHALFKAMS HMLCIGYGQQ APV GMPDVW LTMLSMIVGA TCYAMFIGHA TALIQSLDSS RRQYQEKYKQ VEQYMSFHKL PADTRQRIHE YYEHRYQGKM FDEE SILGE LSEPLREEII NFTCRGLVAH MPLFAHADPS FVTAVLTKLR FEVFQPGDLV VREGSVGRKM YFIQHGLLSV LARGA RDTR LTDGSYFGEI CLLTRGRRTA SVRADTYCRL YSLSVDHFNA VLEEFPMMRR AFETVAMDRL LRIGKKNSIL QRKRSE PSP GSSGGIMEQH LVQHDRDMAR GVRGRAPSTG AQLSGKPVLW EPLVHAPLQA AAVTSNVAIA LTHQRGPLPL SPDSPAT LL ARSAWRSAGS PASPLVPVRA GPWASTSRLP APPARTLHAS LSRAGRSQVS LLGPPPGGGG RRLGPRGRPL SASQPSLP Q RATGDGSPGR KGSGSERLPP SGLLAKPPRT AQPPRPPVPE PATPRGLQLS ANM

UniProtKB: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 3

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Macromolecule #2: 3-[[(3~{S})-1-[2-(3,4-dimethoxyphenyl)ethyl]piperidin-3-yl]methyl...

MacromoleculeName: 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
type: ligand / ID: 2 / Number of copies: 4 / Formula: VXI
Molecular weightTheoretical: 482.612 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.02 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 121387
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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