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Yorodumi- PDB-2vt4: TURKEY BETA1 ADRENERGIC RECEPTOR WITH STABILISING MUTATIONS AND B... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vt4 | ||||||
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Title | TURKEY BETA1 ADRENERGIC RECEPTOR WITH STABILISING MUTATIONS AND BOUND CYANOPINDOLOL | ||||||
Components | BETA1 ADRENERGIC RECEPTOR | ||||||
Keywords | RECEPTOR / GPCR / MEMBRANE / PALMITATE / TRANSDUCER / ANTAGONIST BOUND FORM / INTEGRAL MEMBRANE PROTEIN / G-PROTEIN COUPLED RECEPTOR / G PROTEIN COUPLED RECEPTOR / THERMOSTABILISING POINT MUTATIONS / PHOSPHOPROTEIN / SEVEN-HELIX RECEPTOR / LIPOPROTEIN / 7TM RECEPTOR / GLYCOPROTEIN / TRANSMEMBRANE | ||||||
Function / homology | Function and homology information beta1-adrenergic receptor activity / positive regulation of heart rate by epinephrine-norepinephrine / regulation of circadian sleep/wake cycle, sleep / norepinephrine-epinephrine-mediated vasodilation involved in regulation of systemic arterial blood pressure / adenylate cyclase-activating adrenergic receptor signaling pathway / early endosome / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | MELEAGRIS GALLOPAVO (turkey) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Warne, A. / Serrano-Vega, M.J. / Baker, J.G. / Moukhametzianov, R. / Edwards, P.C. / Henderson, R. / Leslie, A.G.W. / Tate, C.G. / Schertler, G.F.X. | ||||||
Citation | Journal: Nature / Year: 2008 Title: Structure of a Beta1-Adrenergic G-Protein-Coupled Receptor. Authors: Warne, A. / Serrano-Vega, M.J. / Baker, J.G. / Moukhametzianov, R. / Edwards, P.C. / Henderson, R. / Leslie, A.G.W. / Tate, C.G. / Schertler, G.F.X. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2008 Title: Conformational Thermostabilisation of the Beta1-Adrenergic Receptor in a Detergent Resistant Form Authors: Serrano-Vega, M.J. / Magnani, F. / Shibata, Y. / Tate, C.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vt4.cif.gz | 233.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vt4.ent.gz | 188 KB | Display | PDB format |
PDBx/mmJSON format | 2vt4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2vt4_validation.pdf.gz | 3.2 MB | Display | wwPDB validaton report |
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Full document | 2vt4_full_validation.pdf.gz | 3.1 MB | Display | |
Data in XML | 2vt4_validation.xml.gz | 43.9 KB | Display | |
Data in CIF | 2vt4_validation.cif.gz | 57.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vt/2vt4 ftp://data.pdbj.org/pub/pdb/validation_reports/vt/2vt4 | HTTPS FTP |
-Related structure data
Related structure data | 2rh1S 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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3 |
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4 |
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5 |
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6 |
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Unit cell |
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-Components
-Protein / Sugars , 2 types, 16 molecules ABCD
#1: Protein | Mass: 35752.598 Da / Num. of mol.: 4 / Fragment: RESIDUES 33-243,272-276,279-367 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) MELEAGRIS GALLOPAVO (turkey) / Cell: ERYTHROCYTE / Plasmid: PBACPAK8 / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: P07700 #4: Sugar | ChemComp-SOG / |
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-Non-polymers , 4 types, 41 molecules
#2: Chemical | ChemComp-P32 / #3: Chemical | ChemComp-NA / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Compound details | ENGINEERED RESIDUE IN CHAIN A, ARG 68 TO SER ENGINEERED RESIDUE IN CHAIN A, MET 90 TO VAL ...ENGINEERED |
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Sequence details | RESIDUES 3-32 AT THE N-TERMINUS AND RESIDUES 244-271 AND 277-278 OF THE THIRD INTRCELLULAR LOOP ...RESIDUES 3-32 AT THE N-TERMINUS AND RESIDUES 244-271 AND 277-278 OF THE THIRD INTRCELLUL |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.94 Å3/Da / Density % sol: 58 % Description: THE LYSOZYME COMPONENT OF 2RH1 WAS REMOVED FOR THE MOLECULAR REPLACEMENT |
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Crystal grow | Method: vapor diffusion / pH: 7.1 Details: VAPOUR DIFFUSION. EQUAL VOLUMES OF PROTEIN (6MG/ML) IN 10MM TRIS-HCL PH7.7, 50MM NACL, 0.1MM EDTA, 0.35% OCTYLTHIOGLUCOSIDE, 0.5MM CYANOPINDOLOL AND RESERVOIR 0.1M ADA, PH 6.9-7.3, 29-32% PEG600. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 14, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→46.4 Å / Num. obs: 41499 / % possible obs: 96.2 % / Observed criterion σ(I): 0 / Redundancy: 1.8 % / Biso Wilson estimate: 39.32 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 5.8 |
Reflection shell | Resolution: 2.7→2.85 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 1.5 / % possible all: 95.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2RH1 Resolution: 2.7→45.1 Å / SU ML: 0.44 / Phase error: 25.37 / Stereochemistry target values: ML Details: STRICT NCS, SIGMA 0.025, APPLIED TO CHAINS A AND D AND TO CHAINS B AND C, EXCLUDING DETERGENTS
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.82 Å2 / ksol: 0.343 e/Å3 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.32 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→45.1 Å
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Refine LS restraints |
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