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- PDB-5mzp: Crystal structure of stabilized A2A adenosine receptor A2AR-StaR2... -

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Basic information

Entry
Database: PDB / ID: 5mzp
TitleCrystal structure of stabilized A2A adenosine receptor A2AR-StaR2-bRIL in complex with caffeine at 2.1A resolution
ComponentsAdenosine receptor A2a,Soluble cytochrome b562,Adenosine receptor A2a
KeywordsMEMBRANE PROTEIN / G-PROTEIN-COUPLED RECEPTOR / INTEGRAL MEMBRANE PROTEIN / CHIMERA / THERMOSTABILIZING MUTATIONS
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 / positive regulation of protein secretion / regulation of mitochondrial membrane potential / excitatory postsynaptic potential / synaptic transmission, glutamatergic / locomotory behavior / apoptotic signaling pathway / electron transport chain / 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 / phospholipase C-activating G protein-coupled receptor signaling pathway / negative regulation of neuron apoptotic process / postsynaptic membrane / calmodulin binding / periplasmic space / electron transfer activity / positive regulation of ERK1 and ERK2 cascade / iron ion binding / response to xenobiotic stimulus / inflammatory response / negative regulation of cell population proliferation / neuronal cell body / apoptotic process / heme binding / 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 / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / 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)
Similarity search - Domain/homology
CAFFEINE / CHOLESTEROL / OLEIC ACID / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / D(-)-TARTARIC ACID / Soluble cytochrome b562 / Adenosine receptor A2a
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsCheng, K.Y.R. / Segala, E. / Robertson, N. / Deflorian, F. / Dore, A.S. / Errey, J.C. / Fiez-Vandal, C. / Marshall, F.H. / Cooke, R.M.
CitationJournal: Structure / Year: 2017
Title: Structures of Human A1 and A2A Adenosine Receptors with Xanthines Reveal Determinants of Selectivity.
Authors: Cheng, R.K.Y. / Segala, E. / Robertson, N. / Deflorian, F. / Dore, A.S. / Errey, J.C. / Fiez-Vandal, C. / Marshall, F.H. / Cooke, R.M.
History
DepositionFeb 1, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 26, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
Revision 1.3Oct 16, 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,Soluble cytochrome b562,Adenosine receptor A2a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,49133
Polymers47,9971
Non-polymers9,49432
Water3,189177
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10830 Å2
ΔGint40 kcal/mol
Surface area21390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.442, 179.870, 139.640
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Adenosine receptor A2a,Soluble cytochrome b562,Adenosine receptor A2a / Cytochrome b-562


Mass: 47996.746 Da / Num. of mol.: 1
Mutation: A54L, T88A, R107A, K122A, N154A, L202A, M1007W, L235A, V239A, S277A, G318A,A54L, T88A, R107A, K122A, N154A, L202A, M1007W, L235A, V239A, S277A, G318A,A54L, T88A, R107A, K122A, N154A, L202A, ...Mutation: A54L, T88A, R107A, K122A, N154A, L202A, M1007W, L235A, V239A, S277A, G318A,A54L, T88A, R107A, K122A, N154A, L202A, M1007W, L235A, V239A, S277A, G318A,A54L, T88A, R107A, K122A, N154A, L202A, M1007W, L235A, V239A, S277A, G318A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Escherichia coli (E. coli)
Gene: ADORA2A, ADORA2, cybC / Plasmid: PFAST-BAC / Production host: Trichoplusia ni (cabbage looper) / Variant (production host): Tni PRO / References: UniProt: P29274, UniProt: P0ABE7

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Non-polymers , 7 types, 209 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CFF / CAFFEINE / 3,7-DIHYDRO-1,3,7-TRIMETHYL-1H-PURINE-2,6-DIONE


Mass: 194.191 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10N4O2 / Comment: medication*YM
#4: Chemical
ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H46O
#5: Chemical
ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C18H34O2
#6: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C21H40O4
#7: Chemical ChemComp-TAR / D(-)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.58 Å3/Da / Density % sol: 52.36 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 5.5
Details: 0.1M MES PH 5.5, 0.2M K/NA TARTRATE, 27.5-40% PEG400, 0.5-1% (V/V) (+/-)-2-METHYL-2,4-PENTANEDIOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96862 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 25, 2016 / Details: (DOUBLE) KB MIRROR PAIR
RadiationMonochromator: DOUBLE SI (111) CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96862 Å / Relative weight: 1
ReflectionResolution: 2.1→89.94 Å / Num. obs: 29678 / % possible obs: 98.7 % / Redundancy: 4.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.13 / Net I/σ(I): 8.2
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.977 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2379 / CC1/2: 0.454 / Rpim(I) all: 0.532 / % possible all: 99.9

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Processing

Software
NameVersionClassification
XDSv1.0data reduction
Aimless6.5.019data scaling
PHENIX(1.10.1_2155: ???)refinement
PHASER2.5.7phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IU4

5iu4


Resolution: 2.1→38.527 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.33
RfactorNum. reflection% reflection
Rfree0.2199 1479 5.06 %
Rwork0.1955 --
obs0.1967 29222 98.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→38.527 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3010 0 535 177 3722
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0273665
X-RAY DIFFRACTIONf_angle_d0.9534890
X-RAY DIFFRACTIONf_dihedral_angle_d19.6551224
X-RAY DIFFRACTIONf_chiral_restr0.072545
X-RAY DIFFRACTIONf_plane_restr0.006576
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.16780.34161200.27682520X-RAY DIFFRACTION100
2.1678-2.24530.26791310.25722507X-RAY DIFFRACTION99
2.2453-2.33520.28931300.2362513X-RAY DIFFRACTION100
2.3352-2.44140.22691560.22062485X-RAY DIFFRACTION99
2.4414-2.57010.22391430.21152495X-RAY DIFFRACTION99
2.5701-2.73110.21981200.19922494X-RAY DIFFRACTION98
2.7311-2.94190.24391150.19562507X-RAY DIFFRACTION98
2.9419-3.23780.21171400.19642506X-RAY DIFFRACTION99
3.2378-3.7060.23511340.17792559X-RAY DIFFRACTION99
3.706-4.66790.19671440.16032521X-RAY DIFFRACTION97
4.6679-38.53310.18711460.1932636X-RAY DIFFRACTION96
Refinement TLS params.

S33: -0 Å ° / 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 °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.30290.02410.05720.12410.24310.4225-0.0406-0.06120.0316-0.02190.01090.01440.0447-0.11030.1059-0.0111-0.0110.12890.01180.0874-26.0404-3.727820.8347
20.0879-0.23350.13580.1217-0.2596-0.18550.03910.0622-0.0496-0.2691-0.001-0.086-0.03260.00850.16140.03330.00640.1053-0.0230.2147-8.4847-31.746216.248
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 186 )
2X-RAY DIFFRACTION2chain 'A' and (resid 187 through 305 )

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