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- PDB-5k2c: 1.9 angstrom A2a adenosine receptor structure with sulfur SAD pha... -

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Basic information

Entry
Database: PDB / ID: 5k2c
Title1.9 angstrom A2a adenosine receptor structure with sulfur SAD phasing and phase extension using XFEL data
ComponentsAdenosine receptor A2a/Soluble cytochrome b562 chimera
KeywordsMEMBRANE PROTEIN / A2a Adenosine Receptor / sulfur SAD / GPCR / Structural Genomics / PSI-Biology / GPCR Network
Function / homology
Function and homology information


positive regulation of acetylcholine secretion, neurotransmission / regulation of norepinephrine secretion / positive regulation of circadian sleep/wake cycle, sleep / Adenosine P1 receptors / negative regulation of alpha-beta T cell activation / G protein-coupled adenosine receptor activity / G protein-coupled adenosine receptor signaling pathway / response to purine-containing compound / sensory perception / positive regulation of urine volume ...positive regulation of acetylcholine secretion, neurotransmission / regulation of norepinephrine secretion / positive regulation of circadian sleep/wake cycle, sleep / Adenosine P1 receptors / negative regulation of alpha-beta T cell activation / G protein-coupled adenosine receptor activity / G protein-coupled adenosine receptor signaling pathway / response to purine-containing compound / sensory perception / positive regulation of urine volume / NGF-independant TRKA activation / Surfactant metabolism / protein kinase C-activating G protein-coupled receptor signaling pathway / synaptic transmission, dopaminergic / synaptic transmission, cholinergic / inhibitory postsynaptic potential / negative regulation of vascular permeability / type 5 metabotropic glutamate receptor binding / positive regulation of glutamate secretion / blood circulation / intermediate filament / response to caffeine / eating behavior / presynaptic active zone / alpha-actinin binding / membrane depolarization / regulation of calcium ion transport / asymmetric synapse / axolemma / response to inorganic substance / cellular defense response / prepulse inhibition / phagocytosis / positive regulation of apoptotic signaling pathway / response to amphetamine / excitatory postsynaptic potential / presynaptic modulation of chemical synaptic transmission / positive regulation of synaptic transmission, glutamatergic / neuron projection morphogenesis / regulation of mitochondrial membrane potential / locomotory behavior / synaptic transmission, glutamatergic / central nervous system development / positive regulation of long-term synaptic potentiation / astrocyte activation / apoptotic signaling pathway / positive regulation of synaptic transmission, GABAergic / positive regulation of protein secretion / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / adenylate cyclase-activating G protein-coupled receptor signaling pathway / negative regulation of inflammatory response / vasodilation / blood coagulation / cell-cell signaling / presynaptic membrane / G alpha (s) signalling events / postsynaptic membrane / negative regulation of neuron apoptotic process / electron transfer activity / periplasmic space / calmodulin binding / response to xenobiotic stimulus / inflammatory response / iron ion binding / negative regulation of cell population proliferation / dendrite / neuronal cell body / lipid binding / glutamatergic synapse / apoptotic process / heme binding / protein-containing complex binding / regulation of DNA-templated transcription / enzyme binding / membrane / identical protein binding / 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 / 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 / SAD / 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 1.3Nov 22, 2017Group: Refinement description / Category: software
Revision 1.4Feb 14, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site
Revision 1.5Nov 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
Water1,892105
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 , 7 types, 132 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 / ZM-241,385


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 / 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.: 10 / Source method: obtained synthetically / Formula: C21H40O4
#6: Chemical
ChemComp-OLA / OLEIC ACID / Oleic acid


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


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


Mass: 18.015 Da / Num. of mol.: 105 / Source method: isolated from a natural source / Formula: H2O

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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→24 Å / Num. obs: 41882 / % possible obs: 100 % / Redundancy: 291 % / Biso Wilson estimate: 46.9 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
SHELXDphasing
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→23.437 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 22.75 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2079 1988 4.75 %
Rwork0.1726 --
obs0.1743 41828 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→23.437 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3013 0 415 105 3533
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013598
X-RAY DIFFRACTIONf_angle_d1.1764848
X-RAY DIFFRACTIONf_dihedral_angle_d15.0252166
X-RAY DIFFRACTIONf_chiral_restr0.059558
X-RAY DIFFRACTIONf_plane_restr0.006576
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.94750.43351180.45192815X-RAY DIFFRACTION100
1.9475-2.00010.41541710.4182794X-RAY DIFFRACTION100
2.0001-2.05890.33051260.31672797X-RAY DIFFRACTION100
2.0589-2.12540.28881350.24982835X-RAY DIFFRACTION100
2.1254-2.20130.22181370.22392797X-RAY DIFFRACTION100
2.2013-2.28930.23511580.19662795X-RAY DIFFRACTION100
2.2893-2.39340.22731240.17222860X-RAY DIFFRACTION100
2.3934-2.51950.19541350.15242828X-RAY DIFFRACTION100
2.5195-2.67710.17951670.14162807X-RAY DIFFRACTION100
2.6771-2.88350.151350.13632861X-RAY DIFFRACTION100
2.8835-3.1730.21581440.13992826X-RAY DIFFRACTION100
3.173-3.63070.1651460.14392882X-RAY DIFFRACTION100
3.6307-4.56880.18781350.14422920X-RAY DIFFRACTION100
4.5688-23.43860.21881570.18643023X-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)
11.3440.25440.14452.197-0.14631.7016-0.00820.0495-0.0212-0.07130.0127-0.05490.05220.0898-0.00530.2298-0.00890.01520.2809-0.01070.2133.902184.328850.2567
23.6718-2.86530.99457.97563.03152.91040.3390.3484-0.26070.45110.15460.20840.2985-0.0893-0.56710.7951-0.1141-0.07580.55610.10811.2393-20.770935.76851.4366
31.2956-0.8150.32925.3643-0.49181.73080.0061-0.1086-0.15120.44160.01650.13080.2480.0098-0.0140.2576-0.0310.04560.2658-0.01080.1989-1.637479.219860.4654
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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