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- PDB-4ug2: Thermostabilised HUMAN A2a Receptor with CGS21680 bound -

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Basic information

Entry
Database: PDB / ID: 4ug2
TitleThermostabilised HUMAN A2a Receptor with CGS21680 bound
ComponentsTHERMOSTABILISED HUMAN A2A RECEPTOR
KeywordsSIGNALING PROTEIN / G SEVEN-HELIX RECEPTOR / INTEGRAL MEMBRANE PROTEIN / AGONIST BOUND FORM / THERMOSTABILISING POINT MUTATIONS / GPCR / 7TM RECEPTOR
Function / homology
Function and homology information


regulation of norepinephrine secretion / positive regulation of circadian sleep/wake cycle, sleep / positive regulation of acetylcholine secretion, neurotransmission / negative regulation of alpha-beta T cell activation / 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 circadian sleep/wake cycle, sleep / positive regulation of acetylcholine secretion, neurotransmission / negative regulation of alpha-beta T cell activation / 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 / inhibitory postsynaptic potential / type 5 metabotropic glutamate receptor binding / negative regulation of vascular permeability / positive regulation of glutamate secretion / synaptic transmission, cholinergic / blood circulation / response to caffeine / intermediate filament / eating behavior / alpha-actinin binding / presynaptic active zone / regulation of calcium ion transport / membrane depolarization / asymmetric synapse / axolemma / prepulse inhibition / cellular defense response / phagocytosis / presynaptic modulation of chemical synaptic transmission / response to amphetamine / positive regulation of synaptic transmission, glutamatergic / neuron projection morphogenesis / regulation of mitochondrial membrane potential / central nervous system development / positive regulation of long-term synaptic potentiation / excitatory postsynaptic potential / positive regulation of synaptic transmission, GABAergic / synaptic transmission, glutamatergic / positive regulation of protein secretion / astrocyte activation / locomotory behavior / positive regulation of apoptotic signaling pathway / apoptotic signaling pathway / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / negative regulation of inflammatory response / adenylate cyclase-activating G protein-coupled receptor signaling pathway / vasodilation / blood coagulation / cell-cell signaling / presynaptic membrane / G alpha (s) signalling events / negative regulation of neuron apoptotic process / postsynaptic membrane / calmodulin binding / inflammatory response / response to xenobiotic stimulus / negative regulation of cell population proliferation / neuronal cell body / lipid binding / apoptotic process / dendrite / 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
Chem-NGI / (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Adenosine receptor A2a
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsLebon, G. / Edwards, P.C. / Leslie, A.G.W. / Tate, C.G.
CitationJournal: Mol.Pharmacol. / Year: 2015
Title: Molecular Determinants of Cgs21680 Binding to the Human Adenosine A2A Receptor.
Authors: Lebon, G. / Edwards, P.C. / Leslie, A.G.W. / Tate, C.G.
History
DepositionMar 21, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2015Provider: repository / Type: Initial release
Revision 1.1May 13, 2015Group: Database references
Revision 1.2Apr 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 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 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: THERMOSTABILISED HUMAN A2A RECEPTOR
B: THERMOSTABILISED HUMAN A2A RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,7586
Polymers72,0462
Non-polymers1,7124
Water28816
1
A: THERMOSTABILISED HUMAN A2A RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8793
Polymers36,0231
Non-polymers8562
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: THERMOSTABILISED HUMAN A2A RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8793
Polymers36,0231
Non-polymers8562
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.253, 105.944, 125.861
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein THERMOSTABILISED HUMAN A2A RECEPTOR


Mass: 36022.773 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: THE CONSTRUCT WAS TRUNCATED AFTER RESIDUE 316 OF THE A2A SEQUENCE, BUT HAS AN 9 RESIDUE SEQUENCE THAT INCLUDES A LINKER AND THE TEV CLEAVAGE SEQUENCE (AAAENLYFQ) AT THE C-TERMINUS
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-OLB / (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate


Mass: 356.540 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H40O4
#3: Chemical ChemComp-NGI / 2-[P-(2-CARBOXYETHYL)PHENYLETHYL-AMINO]-5'-N-ETHYLCARBOXAMIDO ADENOSINE


Mass: 499.520 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H29N7O6 / Comment: agonist*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O
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: 2

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 51 % / Description: NONE
Crystal growDetails: 0.1M ADA, PH7.0, 21.6% PEG 600, 10% CHS

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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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.6→54.1 Å / Num. obs: 24037 / % possible obs: 99.2 % / Observed criterion σ(I): 2.3 / Redundancy: 9.7 % / Rmerge(I) obs: 0.19 / Net I/σ(I): 9.4
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 9.8 % / Rmerge(I) obs: 1.04 / Mean I/σ(I) obs: 2.3 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2YDO

2ydo


Resolution: 2.6→125.86 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.879 / SU B: 10.01 / SU ML: 0.219 / Cross valid method: THROUGHOUT / ESU R: 0.63 / ESU R Free: 0.322 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.27116 1234 5.1 %RANDOM
Rwork0.2385 ---
obs0.24016 22761 98.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.63 Å2
Baniso -1Baniso -2Baniso -3
1-1.84 Å20 Å20 Å2
2---0.12 Å20 Å2
3----1.72 Å2
Refinement stepCycle: LAST / Resolution: 2.6→125.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4404 0 122 16 4542
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.024645
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0251.9736330
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3495563
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.32421.902163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.24715706
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9491525
X-RAY DIFFRACTIONr_chiral_restr0.0730.2757
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213367
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
Rfree0.334 88 -
Rwork0.304 1505 -
obs--99.69 %

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