+Open data
-Basic information
Entry | Database: PDB / ID: 3bpz | ||||||
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Title | HCN2-I 443-460 E502K in the presence of cAMP | ||||||
Components | Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2 | ||||||
Keywords | TRANSPORT PROTEIN / CNBD / C-LINKER / PACEMAKER / HCN / HCN2 / CHANNEL / CYCLIC NUCLEOTIDE / CAP / PKA / cAMP / ION CHANNEL / LIGAND / cAMP-binding / Glycoprotein / Ion transport / Ionic channel / Membrane / Nucleotide-binding / Phosphoprotein / Potassium / Potassium channel / Potassium transport / Sodium / Sodium channel / Sodium transport / Transmembrane / Transport / Voltage-gated channel | ||||||
Function / homology | Function and homology information HCN channels / HCN channel complex / intracellularly cAMP-activated cation channel activity / cellular response to cGMP / sodium ion import across plasma membrane / voltage-gated sodium channel activity / regulation of membrane depolarization / potassium ion import across plasma membrane / voltage-gated potassium channel activity / sodium ion transmembrane transport ...HCN channels / HCN channel complex / intracellularly cAMP-activated cation channel activity / cellular response to cGMP / sodium ion import across plasma membrane / voltage-gated sodium channel activity / regulation of membrane depolarization / potassium ion import across plasma membrane / voltage-gated potassium channel activity / sodium ion transmembrane transport / cAMP binding / cellular response to cAMP / somatodendritic compartment / potassium ion transmembrane transport / dendrite membrane / regulation of membrane potential / dendritic shaft / PDZ domain binding / molecular adaptor activity / axon / dendrite / neuronal cell body / protein-containing complex binding / membrane / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å | ||||||
Authors | Craven, K.B. / Olivier, N.B. / Zagotta, W.N. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 Title: C-terminal movement during gating in cyclic nucleotide-modulated channels. Authors: Craven, K.B. / Olivier, N.B. / Zagotta, W.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bpz.cif.gz | 189.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bpz.ent.gz | 147.9 KB | Display | PDB format |
PDBx/mmJSON format | 3bpz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bp/3bpz ftp://data.pdbj.org/pub/pdb/validation_reports/bp/3bpz | 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 23628.146 Da / Num. of mol.: 4 / Fragment: ligand biding domain (residues 443-640) / Mutation: E502K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Hcn2, Bcng2, Hac1 / Plasmid: pETGQ / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O88703 #2: Chemical | ChemComp-CMP / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.96 Å3/Da / Density % sol: 58.39 % |
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Crystal grow | Temperature: 279 K / Method: vapor diffusion / pH: 4.6 Details: PEG 400, SODIUM CITRATE, SODIUM CHLORIDE, DTT, HEPES, 5 mM CAMP, pH 4.6, VAPOR DIFFUSION, temperature 279K |
-Data collection
Diffraction | Mean temperature: 110 K | ||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 0.92 Å | ||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 10, 2003 Details: The X26C beamline optics consist of a channel-cut Si(111) crystal monochromator followed by a doubly focusing toroidal mirror | ||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Channel-cut Si(111) monochromator followed by a doubly focusing toroidal mirror Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.65→50 Å / Num. all: 133824 / Num. obs: 132486 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.9 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 17.6 | ||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1Q43 WITHOUT LIGAND OR E502 SIDE-CHAIN Resolution: 1.65→30 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.938 / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.93 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.693 Å / Total num. of bins used: 20
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