+Open data
-Basic information
Entry | Database: PDB / ID: 2ydv | ||||||
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Title | Thermostabilised HUMAN A2a Receptor with NECA bound | ||||||
Components | ADENOSINE RECEPTOR A2A | ||||||
Keywords | RECEPTOR / G PROTEIN COUPLED RECEPTOR / SEVEN-HELIX RECEPTOR / AGONIST BOUND FORM / THERMOSTABILISING POINT MUTATIONS / GPCR / 7TM RECEPTOR | ||||||
Function / homology | Function and homology information positive regulation of acetylcholine secretion, neurotransmission / positive regulation of circadian sleep/wake cycle, sleep / regulation of norepinephrine secretion / negative regulation of alpha-beta T cell activation / Adenosine P1 receptors / G protein-coupled adenosine receptor activity / G protein-coupled adenosine receptor signaling pathway / response to purine-containing compound / sensory perception / NGF-independant TRKA activation ...positive regulation of acetylcholine secretion, neurotransmission / positive regulation of circadian sleep/wake cycle, sleep / regulation of norepinephrine secretion / negative regulation of alpha-beta T cell activation / Adenosine P1 receptors / G protein-coupled adenosine receptor activity / G protein-coupled adenosine receptor signaling pathway / response to purine-containing compound / sensory perception / NGF-independant TRKA activation / Surfactant metabolism / positive regulation of urine volume / alpha-actinin binding / synaptic transmission, dopaminergic / : / inhibitory postsynaptic potential / negative regulation of vascular permeability / type 5 metabotropic glutamate receptor binding / synaptic transmission, cholinergic / blood circulation / positive regulation of glutamate secretion / response to caffeine / intermediate filament / eating behavior / presynaptic active zone / regulation of calcium ion transport / membrane depolarization / asymmetric synapse / axolemma / : / cellular defense response / positive regulation of synaptic transmission, glutamatergic / prepulse inhibition / phagocytosis / neuron projection morphogenesis / response to amphetamine / presynaptic modulation of chemical synaptic transmission / astrocyte activation / excitatory postsynaptic potential / positive regulation of apoptotic signaling pathway / regulation of mitochondrial membrane potential / synaptic transmission, glutamatergic / positive regulation of long-term synaptic potentiation / central nervous system development / locomotory behavior / positive regulation of synaptic transmission, GABAergic / positive regulation of protein secretion / apoptotic signaling pathway / negative regulation of inflammatory response / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / vasodilation / adenylate cyclase-activating G protein-coupled receptor signaling pathway / blood coagulation / cell-cell signaling / presynaptic membrane / G alpha (s) signalling events / postsynaptic membrane / negative regulation of neuron apoptotic process / calmodulin binding / response to xenobiotic stimulus / inflammatory response / negative regulation of cell population proliferation / neuronal cell body / lipid binding / glutamatergic synapse / dendrite / regulation of DNA-templated transcription / protein-containing complex binding / apoptotic process / enzyme binding / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Lebon, G. / Warne, T. / Edwards, P.C. / Bennett, K. / Langmead, C.J. / Leslie, A.G.W. / Tate, C.G. | ||||||
Citation | Journal: Nature / Year: 2011 Title: Agonist-Bound Adenosine A(2A) Receptor Structures Reveal Common Features of Gpcr Activation. Authors: Lebon, G. / Warne, T. / Edwards, P.C. / Bennett, K. / Langmead, C.J. / Leslie, A.G.W. / Tate, C.G. #1: Journal: J.Mol.Biol. / Year: 2011 Title: Thermostabilisation of an Agonist-Bound Conformation of the Human Adenosine A(2A) Receptor. Authors: Lebon, G. / Bennett, K. / Jazayeri, A. / 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 | 2ydv.cif.gz | 79.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ydv.ent.gz | 59 KB | Display | PDB format |
PDBx/mmJSON format | 2ydv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ydv_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 2ydv_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 2ydv_validation.xml.gz | 14.2 KB | Display | |
Data in CIF | 2ydv_validation.cif.gz | 18.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yd/2ydv ftp://data.pdbj.org/pub/pdb/validation_reports/yd/2ydv | HTTPS FTP |
-Related structure data
Related structure data | 2ydoC 3emlS 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 36022.773 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-317 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: BRAIN / Plasmid: PBACPAK8 / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: P29274 | ||||||
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#2: Chemical | ChemComp-NEC / | ||||||
#3: Sugar | ChemComp-SOG / #4: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, LEU 48 TO ALA ENGINEERED RESIDUE IN CHAIN A, ALA 54 TO LEU ...ENGINEERED | Sequence details | THE CONSTRUCT WAS TRUNCATED AFTER RESIDUE 316 OF THE A2A SEQUENCE. CONSTRUCT CRYSTALLISED CONTAINS ...THE CONSTRUCT WAS TRUNCATED AFTER RESIDUE 316 OF THE A2A SEQUENCE. CONSTRUCT CRYSTALLIS | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.01 Å3/Da / Density % sol: 69.3 % / Description: NONE |
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Crystal grow | pH: 6.4 Details: 0.05 M ADA NAOH, PH 6.4, 23.6% V/V PEG 400, 4% V/V 2-PROPANOL. |
-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: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 14, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→49.41 Å / Num. obs: 17471 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 70.5 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 2.6→2.74 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 1.7 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3EML Resolution: 2.6→79.52 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.929 / SU B: 9.904 / SU ML: 0.215 / Cross valid method: THROUGHOUT / ESU R: 0.374 / ESU R Free: 0.264 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES REFINED INDIVIDUALLY.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 75.146 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→79.52 Å
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