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- PDB-2ydv: Thermostabilised HUMAN A2a Receptor with NECA bound -

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Basic information

Entry
Database: PDB / ID: 2ydv
TitleThermostabilised HUMAN A2a Receptor with NECA bound
ComponentsADENOSINE RECEPTOR A2A
KeywordsRECEPTOR / G PROTEIN COUPLED RECEPTOR / SEVEN-HELIX RECEPTOR / AGONIST BOUND FORM / THERMOSTABILISING POINT MUTATIONS / GPCR / 7TM RECEPTOR
Function / homology
Function and homology information


regulation of norepinephrine secretion / positive regulation of acetylcholine secretion, neurotransmission / negative regulation of alpha-beta T cell activation / positive regulation of circadian sleep/wake cycle, sleep / Adenosine P1 receptors / G protein-coupled adenosine receptor activity / response to purine-containing compound / G protein-coupled adenosine receptor signaling pathway / NGF-independant TRKA activation / Surfactant metabolism ...regulation of norepinephrine secretion / positive regulation of acetylcholine secretion, neurotransmission / negative regulation of alpha-beta T cell activation / positive regulation of circadian sleep/wake cycle, sleep / Adenosine P1 receptors / G protein-coupled adenosine receptor activity / response to purine-containing compound / G protein-coupled adenosine receptor signaling pathway / NGF-independant TRKA activation / Surfactant metabolism / sensory perception / positive regulation of urine volume / synaptic transmission, dopaminergic / type 5 metabotropic glutamate receptor binding / negative regulation of vascular permeability / synaptic transmission, cholinergic / positive regulation of glutamate secretion / intermediate filament / presynaptic active zone / blood circulation / response to caffeine / eating behavior / inhibitory postsynaptic potential / alpha-actinin binding / regulation of calcium ion transport / asymmetric synapse / axolemma / membrane depolarization / phagocytosis / cellular defense response / prepulse inhibition / positive regulation of synaptic transmission, glutamatergic / neuron projection morphogenesis / astrocyte activation / presynaptic modulation of chemical synaptic transmission / response to amphetamine / central nervous system development / positive regulation of long-term synaptic potentiation / positive regulation of apoptotic signaling pathway / positive regulation of synaptic transmission, GABAergic / regulation of mitochondrial membrane potential / positive regulation of protein secretion / excitatory postsynaptic potential / synaptic transmission, glutamatergic / locomotory behavior / apoptotic signaling pathway / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / negative regulation of inflammatory response / vasodilation / adenylate cyclase-activating G protein-coupled receptor signaling pathway / blood coagulation / cell-cell signaling / presynaptic membrane / G alpha (s) signalling events / phospholipase C-activating G protein-coupled receptor signaling pathway / negative regulation of neuron apoptotic process / postsynaptic membrane / calmodulin binding / positive regulation of ERK1 and ERK2 cascade / response to xenobiotic stimulus / inflammatory response / negative regulation of cell population proliferation / neuronal cell body / apoptotic process / dendrite / lipid binding / regulation of DNA-templated transcription / protein-containing complex binding / glutamatergic synapse / enzyme binding / identical protein binding / membrane / plasma membrane
Similarity search - Function
Adenosine A2A receptor / Adenosine receptor / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) ...Adenosine A2A receptor / Adenosine receptor / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
N-ETHYL-5'-CARBOXAMIDO ADENOSINE / Adenosine receptor A2a
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsLebon, 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
DepositionMar 24, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 18, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 16, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2019Group: Data collection / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc / pdbx_database_status
Item: _entity_src_gen.pdbx_host_org_cell_line / _pdbx_database_status.recvd_author_approval
Revision 1.4Jul 29, 2020Group: Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_database_status / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ADENOSINE RECEPTOR A2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8737
Polymers36,0231
Non-polymers1,8506
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.936, 99.551, 79.655
Angle α, β, γ (deg.)90.00, 93.31, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein ADENOSINE RECEPTOR A2A / THERMOSTABILISED HUMAN A2A RECEPTOR


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
#2: Chemical ChemComp-NEC / N-ETHYL-5'-CARBOXAMIDO ADENOSINE


Mass: 308.293 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H16N6O4
#3: Sugar
ChemComp-SOG / octyl 1-thio-beta-D-glucopyranoside / 2-HYDROXYMETHYL-6-OCTYLSULFANYL-TETRAHYDRO-PYRAN-3,4,5-TRIOL / 1-S-OCTYL-BETA-D-THIOGLUCOSIDE / octyl 1-thio-beta-D-glucoside / octyl 1-thio-D-glucoside / octyl 1-thio-glucoside


Type: D-saccharide / Mass: 308.434 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: C14H28O5S / Comment: detergent*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, LEU 48 TO ALA ENGINEERED RESIDUE IN CHAIN A, ALA 54 TO LEU ...ENGINEERED RESIDUE IN CHAIN A, LEU 48 TO ALA ENGINEERED RESIDUE IN CHAIN A, ALA 54 TO LEU ENGINEERED RESIDUE IN CHAIN A, THR 65 TO ALA ENGINEERED RESIDUE IN CHAIN A, GLN 89 TO ALA ENGINEERED RESIDUE IN CHAIN A, ASN 154 TO ALA
Has protein modificationY
Sequence detailsTHE 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 CRYSTALLISED CONTAINS THERMOSTABILISING MUTATIONS L48A, A54L, T65A, Q89A. REMOVAL OF GLYCOSYLATION SITE BY MUTATION N154A. AT C- TERMINUS,THERE IS A LINKER PLUS TEV CLEAVAGE SEQUENCE AAAENLYFQ.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.01 Å3/Da / Density % sol: 69.3 % / Description: NONE
Crystal growpH: 6.4
Details: 0.05 M ADA NAOH, PH 6.4, 23.6% V/V PEG 400, 4% V/V 2-PROPANOL.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 14, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 2.6→2.74 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 1.7 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.6.0100refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3EML

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.
RfactorNum. reflection% reflectionSelection details
Rfree0.25809 947 5.1 %RANDOM
Rwork0.23274 ---
obs0.23413 17471 99.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 75.146 Å2
Baniso -1Baniso -2Baniso -3
1--1.16 Å20 Å2-1.76 Å2
2--0.27 Å20 Å2
3---0.69 Å2
Refinement stepCycle: LAST / Resolution: 2.6→79.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2454 0 122 27 2603
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222637
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0051.9913586
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1615313
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.30622.6897
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.76315403
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9961513
X-RAY DIFFRACTIONr_chiral_restr0.0680.2434
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211869
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 68 -
Rwork0.317 1241 -
obs--98.94 %

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