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Yorodumi- PDB-3etq: X-ray structure of cysteine-free fragment of mHCN2 C-terminal reg... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3etq | ||||||
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Title | X-ray structure of cysteine-free fragment of mHCN2 C-terminal region from amino acids 443-630 including C508N, C584S, and C601S mutations | ||||||
Components | Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2 | ||||||
Keywords | TRANSPORT PROTEIN / HCN / ion channel / cAMP / Cyclic nucleotide binding domain / beta roll / C-linker / 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: 1.9 Å | ||||||
Authors | Flynn, G.E. | ||||||
Citation | Journal: Nat.Methods / Year: 2009 Title: Mapping the structure and conformational movements of proteins with transition metal ion FRET. Authors: Taraska, J.W. / Puljung, M.C. / Olivier, N.B. / Flynn, G.E. / 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 | 3etq.cif.gz | 107.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3etq.ent.gz | 80.7 KB | Display | PDB format |
PDBx/mmJSON format | 3etq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/et/3etq ftp://data.pdbj.org/pub/pdb/validation_reports/et/3etq | HTTPS FTP |
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-Related structure data
Related structure data | 3ffqC 1q5oS S: Starting model for refinement 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 23871.236 Da / Num. of mol.: 2 / Fragment: C-terminal fragment / Mutation: C508N, C584S, C601S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Bcng2, Hac1, Hcn2 / Plasmid: pMalc2T / Production host: Escherichia coli (E. coli) / Strain (production host): Bl-21 (DE3) / References: UniProt: O88703 #2: Chemical | #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: 2.77 Å3/Da / Density % sol: 55.53 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 16% w/v PEG 6000, 500 mM NaCl, 10% glycerol, 100 mM citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 25, 2004 |
Radiation | Monochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. obs: 42653 / % possible obs: 99.5 % / Redundancy: 27.3 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 66.615 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 19.6 % / Rmerge(I) obs: 0.296 / Mean I/σ(I) obs: 8.6 / % possible all: 95.4 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1q5o Resolution: 1.9→30 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.933 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.348 / SU ML: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.54 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.95 Å
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