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Yorodumi- PDB-2qc1: Crystal structure of the extracellular domain of the nicotinic ac... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2qc1 | |||||||||
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Title | Crystal structure of the extracellular domain of the nicotinic acetylcholine receptor 1 subunit bound to alpha-bungarotoxin at 1.9 A resolution | |||||||||
Components |
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Keywords | PROTEIN BINDING / nicotinic acetylcholine receptor / glycosylated protein / beta sandwich / Cys-loop / buried hydrophilic residues | |||||||||
Function / homology | Function and homology information Highly calcium permeable postsynaptic nicotinic acetylcholine receptors / Highly calcium permeable nicotinic acetylcholine receptors / skeletal muscle tissue growth / neuromuscular synaptic transmission / acetylcholine-gated channel complex / acetylcholine receptor inhibitor activity / ion channel regulator activity / excitatory extracellular ligand-gated monoatomic ion channel activity / synaptic transmission, cholinergic / postsynaptic specialization membrane ...Highly calcium permeable postsynaptic nicotinic acetylcholine receptors / Highly calcium permeable nicotinic acetylcholine receptors / skeletal muscle tissue growth / neuromuscular synaptic transmission / acetylcholine-gated channel complex / acetylcholine receptor inhibitor activity / ion channel regulator activity / excitatory extracellular ligand-gated monoatomic ion channel activity / synaptic transmission, cholinergic / postsynaptic specialization membrane / acetylcholine receptor signaling pathway / acetylcholine-gated monoatomic cation-selective channel activity / neuromuscular junction development / muscle cell cellular homeostasis / monoatomic cation transport / membrane depolarization / skeletal muscle contraction / neuronal action potential / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / regulation of membrane potential / response to nicotine / neuromuscular junction / neuron cellular homeostasis / transmembrane signaling receptor activity / toxin activity / neuron projection / synapse / cell surface / extracellular region / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) Bungarus multicinctus (many-banded krait) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å | |||||||||
Authors | Dellisanti, C.D. / Yao, Y. / Stroud, J.C. / Wang, Z. / Chen, L. | |||||||||
Citation | Journal: Nat.Neurosci. / Year: 2007 Title: Crystal structure of the extracellular domain of nAChR alpha1 bound to alpha-bungarotoxin at 1.94 A resolution. Authors: Dellisanti, C.D. / Yao, Y. / Stroud, J.C. / Wang, Z.Z. / Chen, L. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2qc1.cif.gz | 80.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qc1.ent.gz | 57.8 KB | Display | PDB format |
PDBx/mmJSON format | 2qc1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2qc1_validation.pdf.gz | 838.1 KB | Display | wwPDB validaton report |
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Full document | 2qc1_full_validation.pdf.gz | 845.5 KB | Display | |
Data in XML | 2qc1_validation.xml.gz | 16.1 KB | Display | |
Data in CIF | 2qc1_validation.cif.gz | 22.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qc/2qc1 ftp://data.pdbj.org/pub/pdb/validation_reports/qc/2qc1 | HTTPS FTP |
-Related structure data
Related structure data | 2bypS 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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-Components
#1: Protein | Mass: 8033.334 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bungarus multicinctus (many-banded krait) / References: UniProt: P60616 |
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#2: Protein | Mass: 24729.012 Da / Num. of mol.: 1 / Mutation: V8E, W149R, V155A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Chrna1, Acra / Production host: Escherichia coli (E. coli) / References: UniProt: P04756 |
#3: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#4: 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: 2.64 Å3/Da / Density % sol: 53.48 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.1M Na citrate, 18% 2-propanol, 8% PEG 4000, pH 6.0, 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 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 17, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.94→50 Å / Num. all: 26445 / Num. obs: 23030 / % possible obs: 87.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 16 % / Biso Wilson estimate: 7.3 Å2 / Rsym value: 0.09 / Net I/σ(I): 20 |
Reflection shell | Resolution: 1.94→2.06 Å / Redundancy: 5 % / Mean I/σ(I) obs: 4 / Num. unique all: 2601 / Rsym value: 41 / % possible all: 67.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 2BYP Resolution: 1.94→41.59 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 30.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.94→41.59 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.94→2.06 Å
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