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- PDB-5k2d: 1.9A angstrom A2a adenosine receptor structure with MR phasing us... -

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Basic information

Entry
Database: PDB / ID: 5k2d
Title1.9A angstrom A2a adenosine receptor structure with MR phasing using XFEL data
ComponentsAdenosine receptor A2a/Soluble cytochrome b562 chimera
KeywordsMEMBRANE PROTEIN / A2a adenosine receptor / Structural Genomics / PSI-Biology / GPCR Network / GPCR
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 / (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / DI(HYDROXYETHYL)ETHER / Chem-ZMA / Soluble cytochrome b562 / Adenosine receptor A2a
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBatyuk, A. / Galli, L. / Ishchenko, A. / Han, G.W. / Gati, C. / Popov, P. / Lee, M.-Y. / Stauch, B. / White, T.A. / Barty, A. ...Batyuk, A. / Galli, L. / Ishchenko, A. / Han, G.W. / Gati, C. / Popov, P. / Lee, M.-Y. / Stauch, B. / White, T.A. / Barty, A. / Aquila, A. / Hunter, M.S. / Liang, M. / Boutet, S. / Pu, M. / Liu, Z.-J. / Nelson, G. / James, D. / Li, C. / Zhao, Y. / Spence, J.C.H. / Liu, W. / Fromme, P. / Katritch, V. / Weierstall, U. / Stevens, R.C. / Cherezov, V. / GPCR Network (GPCR)
CitationJournal: Sci Adv / Year: 2016
Title: Native phasing of x-ray free-electron laser data for a G protein-coupled receptor.
Authors: Batyuk, A. / Galli, L. / Ishchenko, A. / Han, G.W. / Gati, C. / Popov, P.A. / Lee, M.Y. / Stauch, B. / White, T.A. / Barty, A. / Aquila, A. / Hunter, M.S. / Liang, M. / Boutet, S. / Pu, M. / ...Authors: Batyuk, A. / Galli, L. / Ishchenko, A. / Han, G.W. / Gati, C. / Popov, P.A. / Lee, M.Y. / Stauch, B. / White, T.A. / Barty, A. / Aquila, A. / Hunter, M.S. / Liang, M. / Boutet, S. / Pu, M. / Liu, Z.J. / Nelson, G. / James, D. / Li, C. / Zhao, Y. / Spence, J.C. / Liu, W. / Fromme, P. / Katritch, V. / Weierstall, U. / Stevens, R.C. / Cherezov, V.
History
DepositionMay 18, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2016Group: Database references
Revision 1.2Nov 23, 2016Group: Structure summary
Revision 1.3Feb 14, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site
Revision 1.4Nov 28, 2018Group: Data collection
Category: diffrn / pdbx_serial_crystallography_data_reduction ...diffrn / pdbx_serial_crystallography_data_reduction / pdbx_serial_crystallography_measurement / pdbx_serial_crystallography_sample_delivery / pdbx_serial_crystallography_sample_delivery_injection
Item: _diffrn.pdbx_serial_crystal_experiment
Revision 1.5Sep 27, 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 1.6Oct 23, 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)58,27328
Polymers49,9741
Non-polymers8,29927
Water1,67593
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.360, 180.740, 142.800
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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens, Escherichia coli / Gene: ADORA2A, ADORA2,cybC / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P29274, UniProt: P0ABE7

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Non-polymers , 8 types, 120 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
#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-OLB / (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate


Mass: 356.540 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H40O4
#6: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H40O4
#7: Chemical
ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C18H34O2
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 2.61 Å3/Da / Density % sol: 52.79 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 5
Details: 28 % (v/v) PEG 400, 40 mM sodium thiocyanate and 100 mM sodium citrate buffer pH 5.0

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.27 Å
DetectorType: CS-PAD CXI-1 / Detector: PIXEL / Date: Apr 1, 2015 / Details: K-B mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.27 Å / Relative weight: 1
ReflectionResolution: 1.9→23.437 Å / Num. obs: 41882 / % possible obs: 100 % / Redundancy: 291 % / Biso Wilson estimate: 41 Å2 / Net I/σ(I): 6
Reflection shellResolution: 1.9→2 Å / Redundancy: 62 % / Mean I/σ(I) obs: 0.6 / % possible all: 100
Serial crystallography measurementFocal spot size: 1.5 µm2 / Photons per pulse: 64000000000 Tphotons/pulse / Pulse duration: 35 fsec. / Pulse energy: 2.18 µJ / Pulse photon energy: 9.8 keV / XFEL pulse repetition rate: 120 Hz
Serial crystallography sample deliveryMethod: injection
Serial crystallography sample delivery injectionFlow rate: 220 µL/min
Serial crystallography data reductionCrystal hits: 232283 / Frames indexed: 72735 / Frames total: 948961

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EIY

4eiy


Resolution: 1.9→23.44 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 22.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.207 1988 4.75 %
Rwork0.174 --
obs0.176 41828 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→23.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3015 0 422 93 3530
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013616
X-RAY DIFFRACTIONf_angle_d1.1914869
X-RAY DIFFRACTIONf_dihedral_angle_d16.7412182
X-RAY DIFFRACTIONf_chiral_restr0.06558
X-RAY DIFFRACTIONf_plane_restr0.006578
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.94750.42631180.44952815X-RAY DIFFRACTION100
1.9475-2.00010.41671710.41892794X-RAY DIFFRACTION100
2.0001-2.05890.34011260.31832797X-RAY DIFFRACTION100
2.0589-2.12540.29151350.24952835X-RAY DIFFRACTION100
2.1254-2.20130.22251370.22572797X-RAY DIFFRACTION100
2.2013-2.28930.24131580.19812795X-RAY DIFFRACTION100
2.2893-2.39340.2251240.17342860X-RAY DIFFRACTION100
2.3934-2.51950.19341350.15392828X-RAY DIFFRACTION100
2.5195-2.67710.17251670.14282807X-RAY DIFFRACTION100
2.6771-2.88350.15031350.13632861X-RAY DIFFRACTION100
2.8835-3.1730.20571440.14332826X-RAY DIFFRACTION100
3.173-3.63070.17471460.1462882X-RAY DIFFRACTION100
3.6307-4.56880.18591350.14682920X-RAY DIFFRACTION100
4.5688-23.43860.2151570.1883023X-RAY DIFFRACTION100
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)
11.2984-0.2056-0.12732.1352-0.11161.5731-0.0084-0.04540.02850.06390.008-0.0376-0.05790.075-0.00240.23110.0085-0.01270.2734-0.01060.218224.0773186.824321.1302
23.5691.797-1.48128.96132.80167.86310.4544-0.28570.2938-0.34820.17820.2356-0.2620.1361-0.57680.6690.07980.06340.44880.06161.1761-0.7217235.434219.8756
31.36720.7607-0.28755.3108-0.40381.7758-0.00670.10250.192-0.41470.03250.1307-0.3101-0.0033-0.01470.27510.0308-0.04810.2686-0.01370.203318.4771192.269710.8799
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID -2 THROUGH 208 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 1001 THROUGH 1106 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 219 THROUGH 308)

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