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Yorodumi- PDB-4uy2: Crystal structure of the complex of the extracellular domain of h... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4uy2 | ||||||
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Title | Crystal structure of the complex of the extracellular domain of human alpha9 nAChR with alpha-bungarotoxin. | ||||||
Components |
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Keywords | TOXIN-BINDING PROTEIN/TOXIN / TOXIN-BINDING PROTEIN-TOXIN COMPLEX / LIGAND BINDING DOMAIN / CYS-LOOP RECEPTOR | ||||||
Function / homology | Function and homology information Acetylcholine inhibits contraction of outer hair cells / Highly calcium permeable postsynaptic nicotinic acetylcholine receptors / acetylcholine-gated channel complex / detection of mechanical stimulus involved in sensory perception of sound / response to auditory stimulus / acetylcholine receptor inhibitor activity / ion channel regulator activity / acetylcholine-gated monoatomic cation-selective channel activity / inner ear morphogenesis / membrane depolarization ...Acetylcholine inhibits contraction of outer hair cells / Highly calcium permeable postsynaptic nicotinic acetylcholine receptors / acetylcholine-gated channel complex / detection of mechanical stimulus involved in sensory perception of sound / response to auditory stimulus / acetylcholine receptor inhibitor activity / ion channel regulator activity / acetylcholine-gated monoatomic cation-selective channel activity / inner ear morphogenesis / membrane depolarization / transmembrane transporter complex / calcium channel activity / transmembrane signaling receptor activity / toxin activity / positive regulation of cytosolic calcium ion concentration / postsynaptic membrane / neuron projection / synapse / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) BUNGARUS MULTICINCTUS (many-banded krait) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.697 Å | ||||||
Authors | Giastas, P. / Zouridakis, M. / Zarkadas, E. / Tzartos, S.J. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2014 Title: Crystal Structures of Free and Antagonist-Bound States of Human Alpha9 Nicotinic Receptor Extracellular Domain Authors: Zouridakis, M. / Giastas, P. / Zarkadas, E. / Chroni-Tzartou, D. / Bregestovski, P. / Tzartos, S.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4uy2.cif.gz | 240.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4uy2.ent.gz | 196.5 KB | Display | PDB format |
PDBx/mmJSON format | 4uy2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4uy2_validation.pdf.gz | 486.6 KB | Display | wwPDB validaton report |
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Full document | 4uy2_full_validation.pdf.gz | 526.4 KB | Display | |
Data in XML | 4uy2_validation.xml.gz | 27.5 KB | Display | |
Data in CIF | 4uy2_validation.cif.gz | 35.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uy/4uy2 ftp://data.pdbj.org/pub/pdb/validation_reports/uy/4uy2 | HTTPS FTP |
-Related structure data
Related structure data | 4d01C 4uxuC 1d01S 2qc1S 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 25307.029 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR DOMAIN, RESIDUES 26-237 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PPICZAA / Production host: KOMAGATAELLA PASTORIS (fungus) / Strain (production host): X33 / References: UniProt: Q9UGM1 #2: Protein | Mass: 8033.334 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) BUNGARUS MULTICINCTUS (many-banded krait) / References: UniProt: P60616 #3: Sugar | ChemComp-NAG / |
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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: 2.78 Å3/Da / Density % sol: 55.8 % / Description: NONE |
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Crystal grow | pH: 7 Details: 0.1 M MES PH 6.0, 0.2 M NACL, 30% W/V JEFFAMINE ED2003 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 30, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→47 Å / Num. obs: 21021 / % possible obs: 99.5 % / Observed criterion σ(I): 1 / Redundancy: 5.1 % / Biso Wilson estimate: 67.36 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 5.2 % / Rmerge(I) obs: 1.45 / Mean I/σ(I) obs: 1 / % possible all: 97 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 1D01, 2QC1 Resolution: 2.697→47.185 Å / SU ML: 0.54 / σ(F): 1.12 / Phase error: 46.62 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 104 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.697→47.185 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 13.3562 Å / Origin y: -2.5146 Å / Origin z: 7.5095 Å
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Refinement TLS group | Selection details: ALL |