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- EMDB-0094: Structure of human HCN4 hyperpolarization-activated cyclic nucleo... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-0094 | |||||||||
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Title | Structure of human HCN4 hyperpolarization-activated cyclic nucleotide-gated ion channel in complex with cAMP | |||||||||
![]() | Sharpened cryosparc map used for building and refinement | |||||||||
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![]() | ION CHANNEL / PACEMAKER CURRENT / MEMBRANE PROTEIN | |||||||||
Function / homology | ![]() voltage-gated potassium channel activity involved in SA node cell action potential depolarization / sinoatrial node development / HCN channels / HCN channel complex / regulation of cardiac muscle cell action potential involved in regulation of contraction / SA node cell action potential / membrane depolarization during SA node cell action potential / cellular response to cGMP / regulation of membrane depolarization / intracellularly cAMP-activated cation channel activity ...voltage-gated potassium channel activity involved in SA node cell action potential depolarization / sinoatrial node development / HCN channels / HCN channel complex / regulation of cardiac muscle cell action potential involved in regulation of contraction / SA node cell action potential / membrane depolarization during SA node cell action potential / cellular response to cGMP / regulation of membrane depolarization / intracellularly cAMP-activated cation channel activity / membrane depolarization during cardiac muscle cell action potential / sodium ion import across plasma membrane / blood circulation / voltage-gated sodium channel activity / voltage-gated potassium channel activity / monoatomic cation transport / regulation of heart rate by cardiac conduction / potassium ion import across plasma membrane / sodium ion transmembrane transport / regulation of cardiac muscle contraction / cAMP binding / cellular response to cAMP / potassium ion transmembrane transport / regulation of heart rate / muscle contraction / regulation of membrane potential / axon / dendrite / perinuclear region of cytoplasm / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
![]() | Shintre CA / Pike ACW | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of human HCN4 hyperpolarization-activated cyclic nucleotide-gated ion channel Authors: Shintre CA / Pike ACW / Tessitore A / Young M / Bushell SR / Strain-Damerell C / Mukhopadhyay S / Burgess-Brown NA / Huiskonen JT / Arrowsmith CH / Edwards AM / Bountra C / Carpenter EP | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 38.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 22.9 KB 22.9 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 7.8 KB | Display | ![]() |
Images | ![]() | 181.4 KB | ||
Masks | ![]() | 40.6 MB | ![]() | |
Filedesc metadata | ![]() | 6.8 KB | ||
Others | ![]() ![]() ![]() | 20.3 MB 37.2 MB 37.3 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 190.3 KB | Display | ![]() |
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Full document | ![]() | 189.9 KB | Display | |
Data in XML | ![]() | 501 B | Display | |
Data in CIF | ![]() | 370 B | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6gyoMC ![]() 0093C ![]() 6gynC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Sharpened cryosparc map used for building and refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.34 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
-Additional map: Original cryosparc map
File | emd_0094_additional.map | ||||||||||||
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Annotation | Original cryosparc map | ||||||||||||
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Density Histograms |
-Half map: half map1
File | emd_0094_half_map_1.map | ||||||||||||
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Annotation | half map1 | ||||||||||||
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Density Histograms |
-Half map: half map2
File | emd_0094_half_map_2.map | ||||||||||||
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Annotation | half map2 | ||||||||||||
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Density Histograms |
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Sample components
-Entire : Potassium/Sodium hyperpolarization-activated cyclic nucleotide-ga...
Entire | Name: Potassium/Sodium hyperpolarization-activated cyclic nucleotide-gated ion channel 4 |
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Components |
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-Supramolecule #1: Potassium/Sodium hyperpolarization-activated cyclic nucleotide-ga...
Supramolecule | Name: Potassium/Sodium hyperpolarization-activated cyclic nucleotide-gated ion channel 4 type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Potassium/sodium hyperpolarization-activated cyclic nucleotide-ga...
Macromolecule | Name: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4 type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 60.836754 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: SMLPEAEVRL GQAGFMQRQF GAMLQPGVNK FSLRMFGSQK AVEREQERVK SAGFWIIHPY SDFRFYWDLT MLLLMVGNLI IIPVGITFF KDENTTPWIV FNVVSDTFFL IDLVLNFRTG IVVEDNTEII LDPQRIKMKY LKSWFMVDFI SSIPVDYIFL I VETRIDSE ...String: SMLPEAEVRL GQAGFMQRQF GAMLQPGVNK FSLRMFGSQK AVEREQERVK SAGFWIIHPY SDFRFYWDLT MLLLMVGNLI IIPVGITFF KDENTTPWIV FNVVSDTFFL IDLVLNFRTG IVVEDNTEII LDPQRIKMKY LKSWFMVDFI SSIPVDYIFL I VETRIDSE VYKTARALRI VRFTKILSLL RLLRLSRLIR YIHQWEEIFH MTYDLASAVV RIVNLIGMML LLCHWDGCLQ FL VPMLQDF PDDCWVSINN MVNNSWGKQY SYALFKAMSH MLCIGYGRQA PVGMSDVWLT MLSMIVGATC YAMFIGHATA LIQ SLDSSR RQYQEKYKQV EQYMSFHKLP PDTRQRIHDY YEHRYQGKMF DEESILGELS EPLREEIINF NCRKLVASMP LFAN ADPNF VTSMLTKLRF EVFQPGDYII REGTIGKKMY FIQHGVVSVL TKGNKETKLA DGSYFGEICL LTRGRRTASV RADTY CRLY SLSVDNFNEV LEEYPMMRRA FETVALDRLD RIGKKNS UniProtKB: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4 |
-Macromolecule #2: ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE
Macromolecule | Name: ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / type: ligand / ID: 2 / Number of copies: 4 / Formula: CMP |
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Molecular weight | Theoretical: 329.206 Da |
Chemical component information | ![]() ChemComp-CMP: |
-Macromolecule #3: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
Macromolecule | Name: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 3 / Number of copies: 28 / Formula: PC1 |
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Molecular weight | Theoretical: 790.145 Da |
Chemical component information | ![]() ChemComp-PC1: |
-Macromolecule #4: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOINOSITOL
Macromolecule | Name: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOINOSITOL / type: ligand / ID: 4 / Number of copies: 4 / Formula: PIE |
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Molecular weight | Theoretical: 836.061 Da |
Chemical component information | ![]() ChemComp-PIE: |
-Macromolecule #5: 1,2-Distearoyl-sn-glycerophosphoethanolamine
Macromolecule | Name: 1,2-Distearoyl-sn-glycerophosphoethanolamine / type: ligand / ID: 5 / Number of copies: 8 / Formula: 3PE |
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Molecular weight | Theoretical: 748.065 Da |
Chemical component information | ![]() ChemComp-3PE: |
-Macromolecule #6: UNKNOWN ATOM OR ION
Macromolecule | Name: UNKNOWN ATOM OR ION / type: ligand / ID: 6 / Number of copies: 4 / Formula: UNX |
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Molecular weight | Theoretical: 65.409 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 5 mg/mL | ||||||||||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR | ||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV / Details: blotted for 5.5s before plunge. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Details | EBIC TITAN KRIOS M07 |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-48 / Number grids imaged: 1 / Number real images: 2338 / Average exposure time: 16.0 sec. / Average electron dose: 48.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.3 µm / Nominal magnification: 37313 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Details | Initial model was from ligand-free HCN4. Model refined against the cryosparc b-factor sharpened map using default restraints |
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Refinement | Space: REAL / Protocol: AB INITIO MODEL |
Output model | ![]() PDB-6gyo: |