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- PDB-5g53: Structure of the adenosine A2A receptor bound to an engineered G ... -

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Basic information

Entry
Database: PDB / ID: 5g53
TitleStructure of the adenosine A2A receptor bound to an engineered G protein
Components
  • ADENOSINE RECEPTOR A2A
  • ENGINEERED DOMAIN OF HUMAN G ALPHA S LONG ISOFORM
KeywordsSIGNALING PROTEIN / G PROTEIN COUPLED RECEPTOR / ADENOSINE RECEPTOR / SEVEN-HELIX RECEPTOR / INTEGRAL MEMBRANE PROTEIN / GPCR / ENGINEERED G PROTEIN / GPCR-G PROTEIN COMPLEX / MINI-GS
Function / homology
Function and homology information


adenylate cyclase-activating serotonin receptor signaling pathway / 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 / sensory perception of chemical stimulus / response to purine-containing compound / G protein-coupled adenosine receptor signaling pathway ...adenylate cyclase-activating serotonin receptor signaling pathway / 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 / sensory perception of chemical stimulus / response to purine-containing compound / G protein-coupled adenosine receptor signaling pathway / NGF-independant TRKA activation / sensory perception / mu-type opioid receptor binding / Surfactant metabolism / corticotropin-releasing hormone receptor 1 binding / 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 / beta-2 adrenergic receptor binding / response to caffeine / blood circulation / intermediate filament / eating behavior / alpha-actinin binding / presynaptic active zone / regulation of calcium ion transport / PKA activation in glucagon signalling / membrane depolarization / asymmetric synapse / axolemma / hair follicle placode formation / developmental growth / D1 dopamine receptor binding / phagocytosis / intracellular transport / prepulse inhibition / vascular endothelial cell response to laminar fluid shear stress / cellular defense response / renal water homeostasis / Hedgehog 'off' state / adenylate cyclase-activating adrenergic receptor signaling pathway / activation of adenylate cyclase activity / ionotropic glutamate receptor binding / response to prostaglandin E / adenylate cyclase regulator activity / insulin-like growth factor receptor binding / presynaptic modulation of chemical synaptic transmission / response to amphetamine / regulation of insulin secretion / cellular response to glucagon stimulus / positive regulation of synaptic transmission, glutamatergic / adenylate cyclase activator activity / neuron projection morphogenesis / regulation of mitochondrial membrane potential / central nervous system development / positive regulation of apoptotic signaling pathway / trans-Golgi network membrane / positive regulation of long-term synaptic potentiation / excitatory postsynaptic potential / positive regulation of synaptic transmission, GABAergic / synaptic transmission, glutamatergic / positive regulation of protein secretion / locomotory behavior / astrocyte activation / apoptotic signaling pathway / negative regulation of inflammatory response to antigenic stimulus / bone development / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / G-protein beta/gamma-subunit complex binding / negative regulation of inflammatory response / platelet aggregation / cognition / adenylate cyclase-activating G protein-coupled receptor signaling pathway / Prostacyclin signalling through prostacyclin receptor / Glucagon signaling in metabolic regulation / Glucagon-type ligand receptors / Vasopressin regulates renal water homeostasis via Aquaporins / blood coagulation / G alpha (z) signalling events / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / cellular response to catecholamine stimulus / vasodilation / ADORA2B mediated anti-inflammatory cytokines production / adenylate cyclase-activating dopamine receptor signaling pathway / sensory perception of smell / GPER1 signaling / cellular response to prostaglandin E stimulus / heterotrimeric G-protein complex / cell-cell signaling / presynaptic membrane / positive regulation of cold-induced thermogenesis / G protein activity / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / G alpha (i) signalling events / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / G alpha (s) signalling events
Similarity search - Function
Adenosine A2A receptor / Adenosine receptor / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / G-protein alpha subunit, group S / Serpentine type 7TM GPCR chemoreceptor Srsx / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G-alpha domain profile. ...Adenosine A2A receptor / Adenosine receptor / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / G-protein alpha subunit, group S / Serpentine type 7TM GPCR chemoreceptor Srsx / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G-alpha domain profile. / G protein alpha subunit / 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) / P-loop containing nucleotide triphosphate hydrolases / Up-down Bundle / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / N-ETHYL-5'-CARBOXAMIDO ADENOSINE / Adenosine receptor A2a / Guanine nucleotide-binding protein G(s) subunit alpha isoforms short / Guanine nucleotide-binding protein G(s) subunit alpha isoforms XLas
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsCarpenter, B. / Nehme, R. / Warne, T. / Leslie, A.G.W. / Tate, C.G.
Citation
Journal: Nature / Year: 2016
Title: Structure of the Adenosine A2A Receptor Bound to an Engineered G Protein
Authors: Carpenter, B. / Nehme, R. / Warne, T. / Leslie, A.G.W. / Tate, C.G.
#1: Journal: Nature / Year: 2011
Title: Agonist-Bound Adenosine A2A 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.
#2: Journal: Protein Eng. Des. Sel. / Year: 2016
Title: Engineering a minimal G protein to facilitate crystallisation of G protein-coupled receptors in their active conformation.
Authors: Carpenter, B. / Tate, C.G.
History
DepositionMay 19, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 3, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2016Group: Database references
Revision 1.2Aug 24, 2016Group: Database references
Revision 1.3Mar 8, 2017Group: Database references
Revision 1.4Jul 29, 2020Group: Advisory / Derived calculations ...Advisory / Derived calculations / Other / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / 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 1.5Jan 10, 2024Group: 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 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: ADENOSINE RECEPTOR A2A
B: ADENOSINE RECEPTOR A2A
C: ENGINEERED DOMAIN OF HUMAN G ALPHA S LONG ISOFORM
D: ENGINEERED DOMAIN OF HUMAN G ALPHA S LONG ISOFORM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,7469
Polymers123,0694
Non-polymers1,6775
Water00
1
A: ADENOSINE RECEPTOR A2A
C: ENGINEERED DOMAIN OF HUMAN G ALPHA S LONG ISOFORM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,9036
Polymers61,5352
Non-polymers1,3684
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4140 Å2
ΔGint-10 kcal/mol
Surface area23700 Å2
MethodPISA
2
B: ADENOSINE RECEPTOR A2A
D: ENGINEERED DOMAIN OF HUMAN G ALPHA S LONG ISOFORM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,8433
Polymers61,5352
Non-polymers3081
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-12.2 kcal/mol
Surface area22500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.632, 111.814, 161.304
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 ADENOSINE RECEPTOR A2A


Mass: 34909.500 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: THE CONSTRUCT WAS TRUNCATED AFTER RESIDUE 308 OF THE A2A SEQUENCE, BUT HAS A 6 RESIDUE SEQUENCE THAT INCLUDES THE TEV CLEAVAGE SEQUENCE (ENLYFQ) AT THE C- TERMINUS
Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: BRAIN / Plasmid: PBACPAK8 / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: P29274
#2: Protein ENGINEERED DOMAIN OF HUMAN G ALPHA S LONG ISOFORM


Mass: 26625.125 Da / Num. of mol.: 2 / Fragment: RAS DOMAIN, RESIDUES 26-60 AND 847-1037 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: DELETIONS 1-25,65-203,255-264 INSERTION GGSGGSGG LINKING RESIDUES 64 AND 204
Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: BRAIN / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CODONPLUS-RIL / References: UniProt: P63092, UniProt: Q5JWF2
#3: Chemical ChemComp-NEC / N-ETHYL-5'-CARBOXAMIDO ADENOSINE


Mass: 308.293 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H16N6O4
#4: 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.: 2
Source method: isolated from a genetically manipulated source
Formula: C14H28O5S / Comment: detergent*YM
#5: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
Has protein modificationY
Sequence detailsA2A RECEPTOR. THE CONSTRUCT WAS TRUNCATED AFTER RESIDUE 308 OF THE A2A SEQUENCE. REMOVAL OF ...A2A RECEPTOR. THE CONSTRUCT WAS TRUNCATED AFTER RESIDUE 308 OF THE A2A SEQUENCE. REMOVAL OF GLYCOSYLATION SITE BY MUTATION N154A. AT C-TERMINUS,THERE IS A TEV CLEAVAGE SEQUENCE ENLYFQ ENGINEERED G ALPHA S. DELETIONS 1-25, 65-203, 255-264. MUTATIONS G49D, E50N, L63Y, A249D, S252D, L272D, I372A, V375I. INSERTION GGSGGSGG LINKING RESIDUES 64 AND 204. ADDITIONAL G RESIDUE AT N TERMINUS FROM TEV CLEAVAGE SITE.

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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: 2.9 Å3/Da / Density % sol: 58 %
Description: THE RAS DOMAIN FROM ENTRY 3SN6 WAS USED FOR MOLECULAR REPLACEMENT
Crystal growpH: 5.5
Details: 0.1 M NAOAC PH 5.5, 10% PEG 2000 (IN THE PRESENCE OF CHS); OR 0.1 M NAOAC PH 5.7, 9.5% PEG 2000 MME (IN THE ABSENCE OF CHS)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8729
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 9, 2015 / Details: KB MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8729 Å / Relative weight: 1
ReflectionResolution: 3.4→40.3 Å / Num. obs: 20898 / % possible obs: 90.6 % / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Rmerge(I) obs: 0.17 / Net I/σ(I): 3.6
Reflection shellResolution: 3.4→3.49 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 1.2 / % possible all: 78.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0144refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2YDV, 3SN6

2ydv

3sn6


Resolution: 3.4→91.89 Å / Cor.coef. Fo:Fc: 0.828 / Cor.coef. Fo:Fc free: 0.811 / SU B: 46.428 / SU ML: 0.697 / Cross valid method: THROUGHOUT / ESU R Free: 0.69 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY SIDE CHAINS WITHOUT CLEAR ELECTRON DENSITY HAVE BEEN TRUNCATED BACK TO CBETA.
RfactorNum. reflection% reflectionSelection details
Rfree0.31542 1089 5.2 %RANDOM
Rwork0.2837 ---
obs0.28537 19788 89.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 76.297 Å2
Baniso -1Baniso -2Baniso -3
1--1.78 Å20 Å20 Å2
2---3.88 Å20 Å2
3---5.66 Å2
Refinement stepCycle: LAST / Resolution: 3.4→91.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7247 0 112 0 7359
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0197546
X-RAY DIFFRACTIONr_bond_other_d0.0010.027116
X-RAY DIFFRACTIONr_angle_refined_deg1.1491.95810315
X-RAY DIFFRACTIONr_angle_other_deg0.923316166
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2955937
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.50223.024291
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.014151092
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2611533
X-RAY DIFFRACTIONr_chiral_restr0.1150.21234
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028458
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021845
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_it3.027.923781
X-RAY DIFFRACTIONr_mcbond_other3.0217.9193780
X-RAY DIFFRACTIONr_mcangle_it5.20711.8764707
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.2198.0453765
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.94212.0135608
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: 3.4→3.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 64 -
Rwork0.408 903 -
obs--56.48 %

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