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- PDB-5nm4: A2A Adenosine receptor room-temperature structure determined by s... -

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Basic information

Entry
Database: PDB / ID: 5nm4
TitleA2A Adenosine receptor room-temperature structure determined by serial femtosecond crystallography
ComponentsAdenosine receptor A2a,Soluble cytochrome b562,Adenosine receptor A2a
KeywordsSIGNALING PROTEIN / room-temperature / serial crystallography
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 / response to caffeine / blood circulation / eating behavior / inhibitory postsynaptic potential / alpha-actinin binding / regulation of calcium ion transport / asymmetric synapse / axolemma / membrane depolarization / phagocytosis / prepulse inhibition / cellular defense response / positive regulation of synaptic transmission, glutamatergic / neuron projection morphogenesis / presynaptic modulation of chemical synaptic transmission / astrocyte activation / 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 / apoptotic signaling pathway / locomotory behavior / 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 c/b562 / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like ...Adenosine A2A receptor / Adenosine receptor / Cytochrome c/b562 / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / Four Helix Bundle (Hemerythrin (Met), subunit A) / 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) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
CHOLESTEROL / OLEIC ACID / 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: 1.7 Å
AuthorsWeinert, T. / Cheng, R. / James, D. / Gashi, D. / Nogly, P. / Jaeger, K. / Hennig, M. / Standfuss, J.
CitationJournal: Nat Commun / Year: 2017
Title: Serial millisecond crystallography for routine room-temperature structure determination at synchrotrons.
Authors: Weinert, T. / Olieric, N. / Cheng, R. / Brunle, S. / James, D. / Ozerov, D. / Gashi, D. / Vera, L. / Marsh, M. / Jaeger, K. / Dworkowski, F. / Panepucci, E. / Basu, S. / Skopintsev, P. / ...Authors: Weinert, T. / Olieric, N. / Cheng, R. / Brunle, S. / James, D. / Ozerov, D. / Gashi, D. / Vera, L. / Marsh, M. / Jaeger, K. / Dworkowski, F. / Panepucci, E. / Basu, S. / Skopintsev, P. / Dore, A.S. / Geng, T. / Cooke, R.M. / Liang, M. / Prota, A.E. / Panneels, V. / Nogly, P. / Ermler, U. / Schertler, G. / Hennig, M. / Steinmetz, M.O. / Wang, M. / Standfuss, J.
History
DepositionApr 5, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 27, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Nov 14, 2018Group: Data collection / Category: diffrn / Item: _diffrn.pdbx_serial_crystal_experiment
Revision 1.3Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)50,92911
Polymers47,9971
Non-polymers2,93310
Water1,06359
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5080 Å2
ΔGint19 kcal/mol
Surface area19480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.890, 179.150, 141.200
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
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 , 5 types, 69 molecules

#2: Chemical
ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C18H34O2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: 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
#5: Chemical ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C27H46O
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.7 Å3/Da / Density % sol: 54.41 %
Crystal growTemperature: 291 K / Method: lipidic cubic phase / pH: 5
Details: 0.1M sodium citrate pH 5.0, 0.05M sodium thiocyanate, 28-34% PEG400, 5 mM ZM241385, 2% (v/v) 1,6-hexanediol

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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: 1.3 Å
DetectorType: CS-PAD CXI-2 / Detector: PIXEL / Date: Jul 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3 Å / Relative weight: 1
ReflectionResolution: 1.7→20.2 Å / Num. obs: 56793 / % possible obs: 93.7 % / Redundancy: 23.3 % / CC1/2: 0.97 / R split: 0.1794 / Net I/σ(I): 2.93
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 3 % / Mean I/σ(I) obs: 0.44 / Num. unique obs: 3138 / CC1/2: 0.11 / R split: 3.1796 / % possible all: 53.59

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
CrystFELdata reduction
CrystFELdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→19.587 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2354 2606 4.89 %
Rwork0.2123 --
obs0.2134 53302 94.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→19.587 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2844 0 199 59 3102
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133183
X-RAY DIFFRACTIONf_angle_d1.1394362
X-RAY DIFFRACTIONf_dihedral_angle_d14.6491919
X-RAY DIFFRACTIONf_chiral_restr0.057529
X-RAY DIFFRACTIONf_plane_restr0.009527
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.73090.5123740.43951382X-RAY DIFFRACTION49
1.7309-1.76420.37051070.4122129X-RAY DIFFRACTION77
1.7642-1.80020.40321250.39412416X-RAY DIFFRACTION87
1.8002-1.83930.39191310.372564X-RAY DIFFRACTION93
1.8393-1.8820.37151360.35932659X-RAY DIFFRACTION96
1.882-1.92910.34181430.33852729X-RAY DIFFRACTION98
1.9291-1.98120.36081190.31862809X-RAY DIFFRACTION99
1.9812-2.03940.30581630.28382741X-RAY DIFFRACTION100
2.0394-2.10520.30541380.26252818X-RAY DIFFRACTION100
2.1052-2.18030.27051400.2262768X-RAY DIFFRACTION100
2.1803-2.26750.23271530.21552786X-RAY DIFFRACTION100
2.2675-2.37050.24061440.19142821X-RAY DIFFRACTION100
2.3705-2.49520.21181550.19112821X-RAY DIFFRACTION100
2.4952-2.65120.22671610.17292795X-RAY DIFFRACTION100
2.6512-2.85540.18941420.16922848X-RAY DIFFRACTION100
2.8554-3.14170.19151400.17132812X-RAY DIFFRACTION100
3.1417-3.59380.21151650.17612858X-RAY DIFFRACTION100
3.5938-4.51870.22591320.19462905X-RAY DIFFRACTION100
4.5187-19.58810.24671380.24373035X-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)
11.2877-0.1390.23962.1161-0.39732.01720.01490.0176-0.0694-0.0129-0.0176-0.1010.14410.14440.01380.3939-0.00840.01060.3953-0.01810.28566.306485.961349.9518
25.42647.0515-1.99159.1703-2.5121.02050.01640.2404-0.77680.07240.10780.50420.3662-0.1089-0.3140.7304-0.0572-0.0520.5137-0.06110.9807-17.780757.055851.0262
35.2139-2.51151.33212.66591.44976.75760.33370.1223-0.09490.88570.07750.08520.0138-0.0547-0.10010.6695-0.0779-0.08020.45270.0941.11-21.590632.319849.2025
41.5016-0.19230.32782.40760.2811.24820.0337-0.1506-0.29190.378-0.05240.13520.4154-0.01180.02590.5939-0.04150.05560.45820.0140.3985-3.260477.360758.7467
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 195 )
2X-RAY DIFFRACTION2chain 'A' and (resid 196 through 235 )
3X-RAY DIFFRACTION3chain 'A' and (resid 236 through 318 )
4X-RAY DIFFRACTION4chain 'A' and (resid 319 through 409 )

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