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Yorodumi- PDB-4nty: Cesium sites in the crystal structure of acid-sensing ion channel... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4nty | |||||||||
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Title | Cesium sites in the crystal structure of acid-sensing ion channel in complex with snake toxin | |||||||||
Components |
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Keywords | TRANSPORT PROTEIN/TOXIN / Kunitz / phospholipase A2-like / ion channel / nociception / membrane / TRANSPORT PROTEIN-TOXIN complex | |||||||||
Function / homology | Function and homology information pH-gated monoatomic ion channel activity / Stimuli-sensing channels / ligand-gated sodium channel activity / cellular response to pH / ion channel regulator activity / calcium-dependent phospholipase A2 activity / arachidonate secretion / protein homotrimerization / sodium ion transmembrane transport / phospholipid metabolic process ...pH-gated monoatomic ion channel activity / Stimuli-sensing channels / ligand-gated sodium channel activity / cellular response to pH / ion channel regulator activity / calcium-dependent phospholipase A2 activity / arachidonate secretion / protein homotrimerization / sodium ion transmembrane transport / phospholipid metabolic process / lipid catabolic process / phospholipid binding / fatty acid biosynthetic process / positive regulation of fibroblast proliferation / serine-type endopeptidase inhibitor activity / toxin activity / signaling receptor binding / calcium ion binding / extracellular region / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Gallus gallus (chicken) Micrurus tener tener (cobra) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å | |||||||||
Authors | Baconguis, I. / Bohlen, C.J. / Goehring, A. / Julius, D. / Gouaux, E. | |||||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2014 Title: X-ray structure of Acid-sensing ion channel 1-snake toxin complex reveals open state of a na(+)-selective channel. Authors: Baconguis, I. / Bohlen, C.J. / Goehring, A. / Julius, D. / Gouaux, E. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4nty.cif.gz | 131.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4nty.ent.gz | 105.7 KB | Display | PDB format |
PDBx/mmJSON format | 4nty.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4nty_validation.pdf.gz | 703.7 KB | Display | wwPDB validaton report |
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Full document | 4nty_full_validation.pdf.gz | 710 KB | Display | |
Data in XML | 4nty_validation.xml.gz | 24 KB | Display | |
Data in CIF | 4nty_validation.cif.gz | 32.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nt/4nty ftp://data.pdbj.org/pub/pdb/validation_reports/nt/4nty | HTTPS FTP |
-Related 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
-Protein , 3 types, 3 molecules ABC
#1: Protein | Mass: 51327.352 Da / Num. of mol.: 1 / Fragment: UNP residues 14-463 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Gene: ASIC1, ACCN2 / Cell line (production host): human embryonic kidney cells / Production host: Homo sapiens (human) / References: UniProt: Q1XA76 |
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#2: Protein | Mass: 7117.976 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Micrurus tener tener (cobra) / Production host: Escherichia coli (E. coli) / References: UniProt: G9I929 |
#3: Protein | Mass: 13767.645 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Micrurus tener tener (cobra) / Production host: Escherichia coli (E. coli) / References: UniProt: G9I930 |
-Non-polymers , 4 types, 105 molecules
#4: Chemical | ChemComp-CS / #5: Chemical | ChemComp-CL / | #6: Chemical | ChemComp-PE4 / | #7: Water | ChemComp-HOH / | |
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-Details
Sequence details | MODIFIED RESIDUE |
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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: 3.79 Å3/Da / Density % sol: 67.54 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 100 mM sodium acetate, 6-9% PEG 4000, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.378 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 25, 2012 |
Radiation | Monochromator: Double-crystal, Si(111) liquid N2 cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.378 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→50 Å / Num. obs: 31004 / % possible obs: 99.8 % / Observed criterion σ(I): -3 |
Reflection shell | Resolution: 2.65→2.7 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.654 / Mean I/σ(I) obs: 2.25 / % possible all: 97.7 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→46.044 Å / SU ML: 0.33 / σ(F): 1.97 / Phase error: 25.85 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.65→46.044 Å
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Refine LS restraints |
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LS refinement shell |
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