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- PDB-5om4: Structure of the A2A-StaR2-bRIL562-Compound 4e complex at 1.86A o... -

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Basic information

Entry
Database: PDB / ID: 5om4
TitleStructure of the A2A-StaR2-bRIL562-Compound 4e complex at 1.86A obtained from in meso soaking experiments (24 hour soak).
ComponentsAdenosine receptor A2a,Soluble cytochrome b562,Adenosine receptor A2a
KeywordsMEMBRANE PROTEIN / G-Protein Coupled Receptor / Adenosine 2a receptor / 7 TM integral membrane protein / 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 / regulation of mitochondrial membrane potential / positive regulation of protein secretion / excitatory postsynaptic potential / synaptic transmission, glutamatergic / locomotory behavior / apoptotic signaling pathway / electron transport chain / 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 / periplasmic space / calmodulin binding / 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
CHOLESTEROL / OLEIC ACID / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Chem-T4E / 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 Å
AuthorsRucktooa, P. / Cheng, R.K.Y. / Segala, E. / Geng, T. / Errey, J.C. / Brown, G.A. / Cooke, R. / Marshall, F.H. / Dore, A.S.
Funding support1items
OrganizationGrant numberCountry
European Union115366
CitationJournal: Sci Rep / Year: 2018
Title: Towards high throughput GPCR crystallography: In Meso soaking of Adenosine A2A Receptor crystals.
Authors: Rucktooa, P. / Cheng, R.K.Y. / Segala, E. / Geng, T. / Errey, J.C. / Brown, G.A. / Cooke, R.M. / Marshall, F.H. / Dore, A.S.
History
DepositionJul 28, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 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 1.2Nov 6, 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)58,37734
Polymers48,0681
Non-polymers10,31033
Water2,810156
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Monomeric peak on size exclusion chromatography.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10560 Å2
ΔGint35 kcal/mol
Surface area21050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.465, 179.109, 140.032
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: 48067.824 Da / Num. of mol.: 1
Mutation: A54L; T88A; R107A; K122A; L202A; L235A; V239A; S277A; N154A,A54L; T88A; R107A; K122A; L202A; L235A; V239A; S277A; N154A,A54L; T88A; R107A; K122A; L202A; L235A; V239A; S277A; N154A,A54L; ...Mutation: A54L; T88A; R107A; K122A; L202A; L235A; V239A; S277A; N154A,A54L; T88A; R107A; K122A; L202A; L235A; V239A; S277A; N154A,A54L; T88A; R107A; K122A; L202A; L235A; V239A; S277A; N154A,A54L; T88A; R107A; K122A; L202A; L235A; V239A; S277A; N154A,A54L; T88A; R107A; K122A; L202A; L235A; V239A; S277A; N154A,A54L; T88A; R107A; K122A; L202A; L235A; V239A; S277A; N154A,A54L; T88A; R107A; K122A; L202A; L235A; V239A; S277A; N154A,A54L; T88A; R107A; K122A; L202A; L235A; V239A; S277A; N154A,A54L; T88A; R107A; K122A; L202A; L235A; V239A; S277A; N154A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Escherichia coli (E. coli)
Gene: ADORA2A, ADORA2, cybC / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P29274, UniProt: P0ABE7

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Non-polymers , 6 types, 189 molecules

#2: Chemical ChemComp-T4E / 4-(3-amino-5-phenyl-1,2,4-triazin-6-yl)-2-chlorophenol


Mass: 298.727 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H11ClN4O
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#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.: 16 / 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.: 11 / Source method: isolated from a natural source / Formula: C21H40O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 2.13 Å3/Da / Density % sol: 42.21 %
Crystal growTemperature: 293.15 K / Method: lipidic cubic phase
Details: Crystal growth: 0.l M tri-sodium citrate pH 5.3-5.4, 0.05 M sodium thiocyanate, 29-32% PEG400, 2% (v/v) 2,5-hexanediol and 0.5 mM theophylline Compound 4e was added to the mother liquor to a ...Details: Crystal growth: 0.l M tri-sodium citrate pH 5.3-5.4, 0.05 M sodium thiocyanate, 29-32% PEG400, 2% (v/v) 2,5-hexanediol and 0.5 mM theophylline Compound 4e was added to the mother liquor to a concentration of 0.005 mM for the soaking experiments.
PH range: 5.3-5.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96857 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 30, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96857 Å / Relative weight: 1
ReflectionResolution: 2→32.92 Å / Num. obs: 33687 / % possible obs: 98.4 % / Redundancy: 6.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.137 / Rpim(I) all: 0.059 / Net I/σ(I): 10.3
Reflection shellResolution: 2→2.05 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.508 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2470 / CC1/2: 0.439 / Rpim(I) all: 0.635 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX(1.12rc2_2821: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MZJ

5mzj


Resolution: 2→32.922 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 0.08 / Phase error: 20.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2049 3185 4.99 %
Rwork0.1831 --
obs0.1841 63810 98.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→32.922 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3007 0 592 156 3755
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033741
X-RAY DIFFRACTIONf_angle_d0.9294974
X-RAY DIFFRACTIONf_dihedral_angle_d11.5071916
X-RAY DIFFRACTIONf_chiral_restr0.039543
X-RAY DIFFRACTIONf_plane_restr0.003593
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.02990.37161470.32012683X-RAY DIFFRACTION100
2.0299-2.06160.31931480.30462570X-RAY DIFFRACTION97
2.0616-2.09540.30821460.27982637X-RAY DIFFRACTION98
2.0954-2.13150.30221500.27172601X-RAY DIFFRACTION100
2.1315-2.17020.22351310.2572676X-RAY DIFFRACTION98
2.1702-2.2120.24321500.25182577X-RAY DIFFRACTION97
2.212-2.25710.23941460.23922634X-RAY DIFFRACTION99
2.2571-2.30620.2454980.23452590X-RAY DIFFRACTION95
2.3062-2.35980.25311450.21112612X-RAY DIFFRACTION98
2.3598-2.41880.2261300.19942652X-RAY DIFFRACTION99
2.4188-2.48420.25961900.19952551X-RAY DIFFRACTION96
2.4842-2.55730.22571220.19472617X-RAY DIFFRACTION99
2.5573-2.63980.20191240.1792619X-RAY DIFFRACTION97
2.6398-2.73410.18951410.17172618X-RAY DIFFRACTION99
2.7341-2.84350.20441700.16672619X-RAY DIFFRACTION98
2.8435-2.97280.21851640.1662632X-RAY DIFFRACTION100
2.9728-3.12940.18141240.16952627X-RAY DIFFRACTION99
3.1294-3.32530.18721150.16512721X-RAY DIFFRACTION99
3.3253-3.58180.16291390.15532691X-RAY DIFFRACTION100
3.5818-3.94170.16221300.14462658X-RAY DIFFRACTION100
3.9417-4.51090.15981340.14592659X-RAY DIFFRACTION100
4.5109-5.67850.18531260.16552706X-RAY DIFFRACTION100
5.6785-32.92680.18561150.1792675X-RAY DIFFRACTION99
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)
10.96580.16840.28741.58150.04981.26750.0027-0.0149-0.0841-0.0730.0038-0.00380.1335-0.0836-0.00010.1526-0.0020.00940.22710.00870.121-22.8179-5.981617.6668
21.2811-1.91571.27066.311-2.33034.43190.0016-0.32630.5259-0.3628-0.0076-0.26630.05870.0556-0.0180.41210.0766-0.00010.3254-0.06780.7840.8667-54.664620.1003
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and (resseq -1:208 or resseq 219:305 or resseq 1201))
2X-RAY DIFFRACTION2(chain A and (resseq 1001:1106))

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