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Yorodumi- PDB-1q5o: HCN2J 443-645 in the presence of cAMP, selenomethionine derivative -
+Open data
-Basic information
Entry | Database: PDB / ID: 1q5o | ||||||
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Title | HCN2J 443-645 in the presence of cAMP, selenomethionine derivative | ||||||
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 | ||||||
Function / homology | Function and homology information HCN channels / HCN channel complex / ammonium transmembrane transport / 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 ...HCN channels / HCN channel complex / ammonium transmembrane transport / 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 / regulation of membrane potential / dendritic shaft / PDZ domain binding / 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: 2.3 Å | ||||||
Authors | Zagotta, W.N. / Olivier, N.B. / Black, K.D. / Young, E.C. / Olson, R. / Gouaux, J.E. | ||||||
Citation | Journal: Nature / Year: 2003 Title: STRUCTURAL BASIS FOR MODULATION AND AGONIST SPECIFICITY OF HCN PACEMAKER CHANNELS Authors: Zagotta, W.N. / Olivier, N.B. / Black, K.D. / Young, E.C. / Olson, R. / Gouaux, J.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1q5o.cif.gz | 58.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1q5o.ent.gz | 41.4 KB | Display | PDB format |
PDBx/mmJSON format | 1q5o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1q5o_validation.pdf.gz | 716.9 KB | Display | wwPDB validaton report |
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Full document | 1q5o_full_validation.pdf.gz | 721.1 KB | Display | |
Data in XML | 1q5o_validation.xml.gz | 11.6 KB | Display | |
Data in CIF | 1q5o_validation.cif.gz | 15.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q5/1q5o ftp://data.pdbj.org/pub/pdb/validation_reports/q5/1q5o | HTTPS FTP |
-Related structure data
Related structure data | 1q3eC 1q43SC 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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Details | The biological assembly is a tetramer. This structure may be generated by applying the symmetry operations: y-1/2,1/2-x,z and -x,1-y,z and 1/2-y,1/2+x,z |
-Components
#1: Protein | Mass: 24567.943 Da / Num. of mol.: 1 / Fragment: Residues 443-645 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: HCN2, BCNG2 OR HAC1 / Organ: brain / Plasmid: pETGQ / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL-21(DE3) / References: UniProt: O88703 |
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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: 2.32 Å3/Da / Density % sol: 46.96 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: PEG 400, sodium citrate, sodium chloride, DTT, HEPES, cAMP, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.96429 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 2, 2002 |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96429 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. all: 13749 / Num. obs: 13749 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.5 % / Biso Wilson estimate: 23.85 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 23.62 |
Reflection shell | Resolution: 2.3→2.44 Å / % possible all: 99.5 |
Reflection | *PLUS |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1Q43 Resolution: 2.3→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters |
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.033
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Xplor file |
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Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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