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- PDB-5vra: 2.35-Angstrom In situ Mylar structure of human A2A adenosine rece... -

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Basic information

Entry
Database: PDB / ID: 5vra
Title2.35-Angstrom In situ Mylar structure of human A2A adenosine receptor at 100 K
ComponentsAdenosine receptor A2a,Soluble cytochrome b562 chimera
KeywordsSIGNALING PROTEIN / In situ / GPCR / 7TM / LCP / fusion protein
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 / synaptic transmission, dopaminergic / type 5 metabotropic glutamate receptor binding / negative regulation of vascular permeability / synaptic transmission, cholinergic / intermediate filament / presynaptic active zone / positive regulation of glutamate secretion / positive regulation of urine volume / blood circulation / response to caffeine / eating behavior / inhibitory postsynaptic potential / alpha-actinin binding / regulation of calcium ion transport / asymmetric synapse / axolemma / membrane depolarization / prepulse inhibition / cellular defense response / phagocytosis / positive regulation of synaptic transmission, glutamatergic / neuron projection morphogenesis / astrocyte activation / presynaptic modulation of chemical synaptic transmission / central nervous system development / response to amphetamine / positive regulation of long-term synaptic potentiation / positive regulation of synaptic transmission, GABAergic / positive regulation of protein secretion / regulation of mitochondrial membrane potential / positive regulation of apoptotic signaling pathway / synaptic transmission, glutamatergic / excitatory postsynaptic potential / locomotory behavior / apoptotic signaling pathway / electron transport chain / negative regulation of inflammatory response / vasodilation / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / 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 / electron transfer activity / periplasmic space / 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 / regulation of DNA-templated transcription / lipid binding / 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. / 7 transmembrane receptor (rhodopsin family) / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile.
Similarity search - Domain/homology
CHOLESTEROL / OLEIC ACID / (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Chem-ZMA / Soluble cytochrome b562 / Adenosine receptor A2a
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsBroecker, J. / Morizumi, T. / Ou, W.-L. / Klingel, V. / Kuo, A. / Kissick, D.J. / Ishchenko, A. / Lee, M.-Y. / Xu, S. / Makarov, O. ...Broecker, J. / Morizumi, T. / Ou, W.-L. / Klingel, V. / Kuo, A. / Kissick, D.J. / Ishchenko, A. / Lee, M.-Y. / Xu, S. / Makarov, O. / Cherezov, V. / Ogata, C.M. / Ernst, O.P.
Funding support Germany, Canada, United States, 3items
OrganizationGrant numberCountry
German Research Foundation (DFG)BR 5124/1-1 Germany
Canada Excellence Research Chair Award Canada
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM108635 United States
CitationJournal: Nat Protoc / Year: 2018
Title: High-throughput in situ X-ray screening of and data collection from protein crystals at room temperature and under cryogenic conditions.
Authors: Broecker, J. / Morizumi, T. / Ou, W.L. / Klingel, V. / Kuo, A. / Kissick, D.J. / Ishchenko, A. / Lee, M.Y. / Xu, S. / Makarov, O. / Cherezov, V. / Ogata, C.M. / Ernst, O.P.
History
DepositionMay 10, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_volume ..._citation.country / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 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,Soluble cytochrome b562 chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,81523
Polymers49,9741
Non-polymers6,84122
Water1,69394
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.820, 178.900, 140.190
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 chimera / Cytochrome b-562


Mass: 49974.281 Da / Num. of mol.: 1
Fragment: UNP P29274 residues 2-208 and 219-316 linked by UNP P0ABE7 residues 23-128
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: Spodoptera frugiperda (fall armyworm) / References: UniProt: P29274, UniProt: P0ABE7

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Non-polymers , 7 types, 116 molecules

#2: 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
#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.: 3 / Source method: obtained synthetically / Formula: C27H46O
#5: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H40O4
#6: Chemical
ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C18H34O2
#7: Chemical ChemComp-OLB / (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate


Mass: 356.540 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H40O4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 2.5 Å3/Da / Density % sol: 50.76 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 5
Details: 25-28% PEG400, 0.04-0.06 M sodium thiocyanate, 2% 2,5-hexanediol, and 100 mM sodium citrate pH 5.0
PH range: 4.6-5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.35→41.53 Å / Num. obs: 19560 / % possible obs: 91 % / Redundancy: 4.1 % / Biso Wilson estimate: 26.53 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.154 / Net I/σ(I): 6.6
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 2 % / Rmerge(I) obs: 0.611 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1384 / CC1/2: 0.56 / % possible all: 68

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EIY

4eiy


Resolution: 2.35→41.419 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2225 979 5.05 %
Rwork0.1982 --
obs0.1995 19390 90.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.35→41.419 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3012 0 371 94 3477
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033555
X-RAY DIFFRACTIONf_angle_d0.7654797
X-RAY DIFFRACTIONf_dihedral_angle_d11.7352162
X-RAY DIFFRACTIONf_chiral_restr0.045551
X-RAY DIFFRACTIONf_plane_restr0.003607
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.47390.26831130.23432083X-RAY DIFFRACTION73
2.4739-2.62890.23651370.20682531X-RAY DIFFRACTION88
2.6289-2.83180.22921400.20142674X-RAY DIFFRACTION93
2.8318-3.11670.22031460.1922745X-RAY DIFFRACTION96
3.1167-3.56750.21911430.19092773X-RAY DIFFRACTION95
3.5675-4.49380.20821490.17262757X-RAY DIFFRACTION94
4.4938-41.4250.22221510.21852848X-RAY DIFFRACTION93
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)
10.6913-0.35650.09530.90710.10380.6534-0.0213-0.0477-0.00930.02610.0275-0.0141-0.0068-0.0142-0.01320.195-0.01120.00950.19380.00780.1642-4.1356-6.363721.0058
20.7378-0.44270.1982.7203-0.4381.14580.0453-0.31710.02040.01260.1229-0.1363-0.03720.1763-0.04590.34930.084-0.00390.30640.00340.642821.1504-54.59919.964
30.53230.16770.26081.9887-0.04670.6286-0.00590.0788-0.0264-0.14790.02480.0060.0741-0.015-0.0040.17160.00780.02630.19270.00950.12061.6502-11.136310.6796
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 1 through 208)
2X-RAY DIFFRACTION2(chain 'A' and resid 1001 through 1106)
3X-RAY DIFFRACTION3(chain 'A' and resid 219 through 307)

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