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Yorodumi- PDB-3otf: Structural basis for the cAMP-dependent gating in human HCN4 channel -
+Open data
-Basic information
Entry | Database: PDB / ID: 3otf | ||||||
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Title | Structural basis for the cAMP-dependent gating in human HCN4 channel | ||||||
Components | Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4 | ||||||
Keywords | TRANSPORT PROTEIN / cyclic-nucleotide binding | ||||||
Function / homology | Function and homology information 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 / intracellularly cAMP-activated cation channel activity / cellular response to cGMP / membrane depolarization during cardiac muscle cell action potential ...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 / intracellularly cAMP-activated cation channel activity / cellular response to cGMP / membrane depolarization during cardiac muscle cell action potential / sodium ion import across plasma membrane / blood circulation / voltage-gated sodium channel activity / regulation of membrane depolarization / potassium ion import across plasma membrane / voltage-gated potassium channel activity / regulation of heart rate by cardiac conduction / monoatomic cation transport / sodium ion transmembrane transport / regulation of cardiac muscle contraction / cAMP binding / cellular response to cAMP / potassium ion transmembrane transport / regulation of heart rate / regulation of membrane potential / muscle contraction / axon / dendrite / perinuclear region of cytoplasm / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Xu, X. / Vysotskaya, Z.V. / Liu, Q. / Zhou, L. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 Title: Structural basis for the cAMP-dependent gating in the human HCN4 channel. Authors: Xu, X. / Vysotskaya, Z.V. / Liu, Q. / Zhou, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3otf.cif.gz | 55.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3otf.ent.gz | 38.6 KB | Display | PDB format |
PDBx/mmJSON format | 3otf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ot/3otf ftp://data.pdbj.org/pub/pdb/validation_reports/ot/3otf | HTTPS FTP |
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-Related structure data
Related structure data | 1q43S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 25888.441 Da / Num. of mol.: 1 Fragment: nucleotide binding domain (CNBD, unp residues 521-739) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HCN4 / Plasmid: pSMT3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3(GOLD) / References: UniProt: Q9Y3Q4 |
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#2: Chemical | ChemComp-CMP / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.32 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 12% ethanol, sodium citrate, 200 mM Li2SO4, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97923 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 2, 2009 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97923 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.4→50 Å / Num. obs: 9567 / % possible obs: 94 % / Rmerge(I) obs: 0.053 / Rsym value: 0.053 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1Q43 Resolution: 2.4→50 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.936 / SU B: 11.927 / SU ML: 0.265 / Cross valid method: THROUGHOUT / ESU R Free: 0.297 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 79.065 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.401→2.463 Å / Total num. of bins used: 20
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