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Yorodumi- PDB-4ntx: Structure of acid-sensing ion channel in complex with snake toxin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ntx | |||||||||
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Title | Structure of acid-sensing ion channel in complex with snake toxin and amiloride | |||||||||
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 : / Stimuli-sensing channels / cellular response to pH / ion channel regulator activity / phospholipase A2 activity / arachidonic acid secretion / protein homotrimerization / sodium ion transmembrane transport / phospholipid metabolic process / lipid catabolic process ...: / Stimuli-sensing channels / cellular response to pH / ion channel regulator activity / phospholipase A2 activity / arachidonic acid secretion / protein homotrimerization / sodium ion transmembrane transport / phospholipid metabolic process / lipid catabolic process / serine-type endopeptidase inhibitor activity / toxin activity / 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: 2.27 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 | 4ntx.cif.gz | 135.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ntx.ent.gz | 107 KB | Display | PDB format |
PDBx/mmJSON format | 4ntx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nt/4ntx ftp://data.pdbj.org/pub/pdb/validation_reports/nt/4ntx | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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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 |
-Sugars , 1 types, 2 molecules
#4: Sugar |
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-Non-polymers , 5 types, 188 molecules
#5: Chemical | ChemComp-CL / | ||||||
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#6: Chemical | #7: Chemical | ChemComp-P6G / | #8: Chemical | #9: Water | ChemComp-HOH / | |
-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: 3.77 Å3/Da / Density % sol: 67.38 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 50 mM sodium acetate, 22-25% PEG 400, 10 mM magnesium acetate, 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 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 18, 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 Å / Relative weight: 1 |
Reflection | Resolution: 1.97→29.25 Å / Num. obs: 71494 / % possible obs: 95.3 % / Observed criterion σ(I): -3 |
Reflection shell | Resolution: 1.97→2.04 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 1.15 / % possible all: 62 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.27→29 Å / SU ML: 0.28 / σ(F): 1.44 / Phase error: 24.93 / 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: 2.27→29 Å
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Refine LS restraints |
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LS refinement shell |
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