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Yorodumi- PDB-6gyo: Structure of human HCN4 hyperpolarization-activated cyclic nucleo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6gyo | |||||||||
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Title | Structure of human HCN4 hyperpolarization-activated cyclic nucleotide-gated ion channel in complex with cAMP | |||||||||
Components | Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4 | |||||||||
Keywords | MEMBRANE PROTEIN / ION CHANNEL / PACEMAKER CURRENT | |||||||||
Function / homology | Function and homology information voltage-gated potassium channel activity involved in SA node cell action potential depolarization / sinoatrial node development / regulation of cardiac muscle cell action potential involved in regulation of contraction / HCN channels / SA node cell action potential / HCN channel complex / membrane depolarization during SA node cell action potential / intracellularly cAMP-activated cation channel activity / cellular response to cGMP / regulation of membrane depolarization ...voltage-gated potassium channel activity involved in SA node cell action potential depolarization / sinoatrial node development / regulation of cardiac muscle cell action potential involved in regulation of contraction / HCN channels / SA node cell action potential / HCN channel complex / membrane depolarization during SA node cell action potential / intracellularly cAMP-activated cation channel activity / cellular response to cGMP / regulation of membrane depolarization / membrane depolarization during cardiac muscle cell action potential / sodium ion import across plasma membrane / blood circulation / voltage-gated sodium channel activity / potassium ion import across plasma membrane / regulation of heart rate by cardiac conduction / monoatomic cation transport / voltage-gated potassium channel activity / regulation of cardiac muscle contraction / sodium ion transmembrane transport / muscle contraction / cellular response to cAMP / cAMP binding / potassium ion transmembrane transport / regulation of heart rate / regulation of membrane potential / axon / dendrite / perinuclear region of cytoplasm / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Shintre, C.A. / Pike, A.C.W. / Tessitore, A. / Young, M. / Bushell, S.R. / Strain-Damerell, C. / Mukhopadhyay, S. / Burgess-Brown, N.A. / Huiskonen, J.T. / Arrowsmith, C.H. ...Shintre, C.A. / Pike, A.C.W. / Tessitore, A. / Young, M. / Bushell, S.R. / Strain-Damerell, C. / Mukhopadhyay, S. / Burgess-Brown, N.A. / Huiskonen, J.T. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Carpenter, E.P. / Structural Genomics Consortium (SGC) | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: To Be Published Title: Structure of human HCN4 hyperpolarization-activated cyclic nucleotide-gated ion channel Authors: Shintre, C.A. / Pike, A.C.W. / Tessitore, A. / Young, M. / Bushell, S.R. / Strain-Damerell, C. / Mukhopadhyay, S. / Burgess-Brown, N.A. / Huiskonen, J.T. / Arrowsmith, C.H. / Edwards, A.M. / ...Authors: Shintre, C.A. / Pike, A.C.W. / Tessitore, A. / Young, M. / Bushell, S.R. / Strain-Damerell, C. / Mukhopadhyay, S. / Burgess-Brown, N.A. / Huiskonen, J.T. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Carpenter, E.P. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6gyo.cif.gz | 395.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6gyo.ent.gz | 322.6 KB | Display | PDB format |
PDBx/mmJSON format | 6gyo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6gyo_validation.pdf.gz | 2.9 MB | Display | wwPDB validaton report |
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Full document | 6gyo_full_validation.pdf.gz | 3 MB | Display | |
Data in XML | 6gyo_validation.xml.gz | 69.6 KB | Display | |
Data in CIF | 6gyo_validation.cif.gz | 100.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gy/6gyo ftp://data.pdbj.org/pub/pdb/validation_reports/gy/6gyo | HTTPS FTP |
-Related structure data
Related structure data | 0094MC 0093C 6gynC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 60836.754 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HCN4 / Plasmid: pFB-LIC-Bse / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9Y3Q4 |
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-Non-polymers , 5 types, 48 molecules
#2: Chemical | ChemComp-CMP / #3: Chemical | ChemComp-PC1 / #4: Chemical | ChemComp-PIE / #5: Chemical | ChemComp-3PE / #6: Chemical | ChemComp-UNX / |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Potassium/Sodium hyperpolarization-activated cyclic nucleotide-gated ion channel 4 Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: RECOMBINANT | ||||||||||||||||||||||||||||||
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Source (natural) | Organism: Homo sapiens (human) | ||||||||||||||||||||||||||||||
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) | ||||||||||||||||||||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 278 K / Details: blotted for 5.5s before plunge |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS / Details: EBIC TITAN KRIOS M07 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 37313 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1300 nm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 16 sec. / Electron dose: 48 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2338 |
Image scans | Movie frames/image: 48 / Used frames/image: 1-48 |
-Processing
Software | Name: PHENIX / Version: 1.13_2998: / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
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EM software |
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Image processing | Details: Images were motioncorrected and dose-weighted with MOTIONCOR2 | ||||||||||||||||||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 234908 Details: Autopicking with templates derived from manually picked particles | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C4 (4 fold cyclic) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 55829 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL Details: Initial model was from ligand-free HCN4. Model refined against the cryosparc b-factor sharpened map using default restraints |