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- PDB-3vga: Crystal structure of human adenosine A2A receptor with an alloste... -

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Basic information

Entry
Database: PDB / ID: 3vga
TitleCrystal structure of human adenosine A2A receptor with an allosteric inverse-agonist antibody at 3.1 A resolution
Components
  • Adenosine receptor A2a
  • antibody fab fragment heavy chain
  • antibody fab fragment light chain
KeywordsSIGNALING PROTEIN / 7 transmembrane receptor / SIGNAL TRANSDUCTION
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 / sensory perception ...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 / sensory perception / Surfactant metabolism / 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 / response to caffeine / blood circulation / intermediate filament / eating behavior / alpha-actinin binding / presynaptic active zone / regulation of calcium ion transport / membrane depolarization / asymmetric synapse / axolemma / phagocytosis / prepulse inhibition / cellular defense response / 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 apoptotic signaling pathway / 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 / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / negative regulation of inflammatory response / adenylate cyclase-activating G protein-coupled receptor signaling pathway / blood coagulation / vasodilation / 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 / positive regulation of ERK1 and ERK2 cascade / calmodulin binding / inflammatory response / response to xenobiotic stimulus / negative regulation of cell population proliferation / neuronal cell body / apoptotic process / lipid binding / 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) / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Chem-ZMA / Adenosine receptor A2a
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsHino, T. / Arakawa, T. / Iwanari, H. / Yurugi-Kobayashi, T. / Ikeda-Suno, C. / Nakada-Nakura, Y. / Kusano-Arai, O. / Weyand, S. / Shimamura, T. / Nomura, N. ...Hino, T. / Arakawa, T. / Iwanari, H. / Yurugi-Kobayashi, T. / Ikeda-Suno, C. / Nakada-Nakura, Y. / Kusano-Arai, O. / Weyand, S. / Shimamura, T. / Nomura, N. / Cameron, A.D. / Kobayashi, T. / Hamakubo, T. / Iwata, S. / Murata, T.
CitationJournal: Nature / Year: 2012
Title: G-protein-coupled receptor inactivation by an allosteric inverse-agonist antibody
Authors: Hino, T. / Arakawa, T. / Iwanari, H. / Yurugi-Kobayashi, T. / Ikeda-Suno, C. / Nakada-Nakura, Y. / Kusano-Arai, O. / Weyand, S. / Shimamura, T. / Nomura, N. / Cameron, A.D. / Kobayashi, T. / ...Authors: Hino, T. / Arakawa, T. / Iwanari, H. / Yurugi-Kobayashi, T. / Ikeda-Suno, C. / Nakada-Nakura, Y. / Kusano-Arai, O. / Weyand, S. / Shimamura, T. / Nomura, N. / Cameron, A.D. / Kobayashi, T. / Hamakubo, T. / Iwata, S. / Murata, T.
History
DepositionAug 4, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 1, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2012Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Adenosine receptor A2a
B: antibody fab fragment light chain
C: antibody fab fragment heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,7004
Polymers84,3633
Non-polymers3371
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6170 Å2
ΔGint-29 kcal/mol
Surface area32820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.313, 89.766, 110.682
Angle α, β, γ (deg.)90.00, 96.14, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-231-

HOH

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Components

#1: Protein Adenosine receptor A2a


Mass: 36540.266 Da / Num. of mol.: 1 / Fragment: UNP residues 1-316 / Mutation: N154Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADORA2A, ADORA2 / Plasmid: pPIC9K / Production host: Pichia pastoris (fungus) / References: UniProt: P29274
#2: Antibody antibody fab fragment light chain


Mass: 23527.910 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Antibody antibody fab fragment heavy chain


Mass: 24294.918 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#4: Chemical ChemComp-ZMA / 4-{2-[(7-amino-2-furan-2-yl[1,2,4]triazolo[1,5-a][1,3,5]triazin-5-yl)amino]ethyl}phenol


Mass: 337.336 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H15N7O2 / Comment: antagonist*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.53 Å3/Da / Density % sol: 65.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 30% PEG 400, 0.1M MES, 0.2M magnesium chloride, 0.5% octhyl thioglucoside , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 7, 2010
RadiationMonochromator: ACCEL Fixed exit Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.1→71.2 Å / Num. all: 18451 / Num. obs: 18451 / % possible obs: 88.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Biso Wilson estimate: 79 Å2 / Rmerge(I) obs: 0.109 / Net I/σ(I): 5.3
Reflection shellResolution: 3.1→3.27 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.636 / Mean I/σ(I) obs: 1.5 / Num. unique all: 2700 / % possible all: 90.4

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VGA

1vga


Resolution: 3.1→19.996 Å / SU ML: 0.83 / σ(F): 1.34 / Phase error: 26.76 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2633 968 5.13 %RANDOM
Rwork0.1959 ---
all0.1992 ---
obs0.1992 17901 88.4 %-
Solvent computationShrinkage radii: 0.27 Å / VDW probe radii: 0.6 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.174 Å2 / ksol: 0.304 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--15.7396 Å20 Å2-9.553 Å2
2--6.8006 Å2-0 Å2
3---8.9391 Å2
Refinement stepCycle: LAST / Resolution: 3.1→19.996 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5596 0 25 14 5635
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085768
X-RAY DIFFRACTIONf_angle_d1.2787850
X-RAY DIFFRACTIONf_dihedral_angle_d17.0532007
X-RAY DIFFRACTIONf_chiral_restr0.084902
X-RAY DIFFRACTIONf_plane_restr0.006980
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.26280.31671410.26142591X-RAY DIFFRACTION90
3.2628-3.46620.28691140.22242575X-RAY DIFFRACTION89
3.4662-3.73230.2461370.20332523X-RAY DIFFRACTION88
3.7323-4.10490.2711580.17792584X-RAY DIFFRACTION90
4.1049-4.69220.22591320.15642498X-RAY DIFFRACTION86
4.6922-5.88660.24511350.17222612X-RAY DIFFRACTION90
5.8866-19.99690.28381510.22522518X-RAY DIFFRACTION85
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.97950.0699-0.60191.47760.34111.77490.0755-0.6853-0.06930.52460.1228-0.6416-0.04170.8520.0461-0.45860.0402-0.27640.8223-0.1037-0.063862.765-8.870836.3356
24.90380.71961.68610.87050.28711.1396-0.24290.11780.6495-0.0755-0.0260.0882-0.20840.08980.22530.3953-0.03640.0060.20130.07750.464519.75081.40670.0609
33.94930.26292.63391.32280.58712.88840.19560.7483-0.0005-0.2767-0.05220.00710.07170.4044-0.15890.31840.09750.03840.3262-0.00990.341720.419-15.9471-4.7868
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A'
2X-RAY DIFFRACTION2chain 'C'
3X-RAY DIFFRACTION3chain 'B'

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