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Yorodumi- PDB-5khk: HCN2 CNBD in complex with 2-aminopurine riboside-3', 5'-cyclic mo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5khk | ||||||
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Title | HCN2 CNBD in complex with 2-aminopurine riboside-3', 5'-cyclic monophosphate (2-NH2-cPuMP) | ||||||
Components | Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2 | ||||||
Keywords | TRANSPORT PROTEIN / protein-ligand complex / cycilc nucleotide binding domain / ion transport | ||||||
Function / homology | Function and homology information HCN channels / HCN channel complex / cellular response to cGMP / regulation of membrane depolarization / intracellularly cAMP-activated cation channel activity / sodium ion import across plasma membrane / voltage-gated sodium channel activity / voltage-gated potassium channel activity / potassium ion import across plasma membrane / sodium ion transmembrane transport ...HCN channels / HCN channel complex / cellular response to cGMP / regulation of membrane depolarization / intracellularly cAMP-activated cation channel activity / sodium ion import across plasma membrane / voltage-gated sodium channel activity / voltage-gated potassium channel activity / potassium ion import across plasma membrane / sodium ion transmembrane transport / cAMP binding / cellular response to cAMP / potassium ion transmembrane transport / somatodendritic compartment / dendrite membrane / dendritic shaft / PDZ domain binding / regulation of membrane potential / molecular adaptor activity / axon / neuronal cell body / dendrite / protein-containing complex binding / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å | ||||||
Authors | Ng, L.C.T. / Putrenko, I. / Baronas, V. / Van Petegem, F. / Accili, E.A. | ||||||
Citation | Journal: Structure / Year: 2016 Title: Cyclic Purine and Pyrimidine Nucleotides Bind to the HCN2 Ion Channel and Variably Promote C-Terminal Domain Interactions and Opening. Authors: Ng, L.C. / Putrenko, I. / Baronas, V. / Van Petegem, F. / Accili, E.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5khk.cif.gz | 59 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5khk.ent.gz | 41.1 KB | Display | PDB format |
PDBx/mmJSON format | 5khk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5khk_validation.pdf.gz | 741.7 KB | Display | wwPDB validaton report |
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Full document | 5khk_full_validation.pdf.gz | 743.4 KB | Display | |
Data in XML | 5khk_validation.xml.gz | 10.6 KB | Display | |
Data in CIF | 5khk_validation.cif.gz | 13.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kh/5khk ftp://data.pdbj.org/pub/pdb/validation_reports/kh/5khk | HTTPS FTP |
-Related structure data
Related structure data | 5khgC 5khhC 5khiC 5khjC 1q5oS C: citing same article (ref.) 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 23883.330 Da / Num. of mol.: 1 / Fragment: UNP residues 443-643 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Hcn2, Bcng2, Hac1 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O88703 |
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#2: Chemical | ChemComp-6SZ / |
#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: 2.29 Å3/Da / Density % sol: 46.18 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 200 mM NaCl, 0.1 mM sodium citrate pH 4.6, 12% PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 22, 2013 / Details: 1000 um thick sensor | ||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.07→38.4 Å / Num. obs: 13521 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 13.86 % / Biso Wilson estimate: 49.461 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.067 / Net I/σ(I): 26.99 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1Q5O Resolution: 2.07→38.4 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.931 / SU B: 5.397 / SU ML: 0.147 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.238 / ESU R Free: 0.199 / Details: molecular replacement
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 105.2 Å2 / Biso mean: 47.952 Å2 / Biso min: 27.76 Å2
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Refinement step | Cycle: final / Resolution: 2.07→38.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.068→2.121 Å / Total num. of bins used: 20
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