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

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Basic information

Entry
Database: PDB / ID: 5nlx
TitleA2A Adenosine receptor room-temperature structure determined by serial millisecond crystallography
ComponentsAdenosine receptor A2a,Soluble cytochrome b562,Adenosine receptor A2a
KeywordsMEMBRANE PROTEIN / room-temperature / serial crystallography / GPCR / HYDROLASE
Function / homology
Function and homology information


regulation of norepinephrine secretion / positive regulation of acetylcholine secretion, neurotransmission / negative regulation of alpha-beta T cell activation / Adenosine P1 receptors / positive regulation of circadian sleep/wake cycle, sleep / G protein-coupled adenosine receptor activity / response to purine-containing compound / G protein-coupled adenosine receptor signaling pathway / NGF-independant TRKA activation / sensory perception ...regulation of norepinephrine secretion / positive regulation of acetylcholine secretion, neurotransmission / negative regulation of alpha-beta T cell activation / Adenosine P1 receptors / positive regulation of circadian sleep/wake cycle, sleep / G protein-coupled adenosine receptor activity / response to purine-containing compound / G protein-coupled adenosine receptor signaling pathway / NGF-independant TRKA activation / sensory perception / Surfactant metabolism / positive regulation of urine volume / synaptic transmission, dopaminergic / type 5 metabotropic glutamate receptor binding / negative regulation of vascular permeability / positive regulation of glutamate secretion / synaptic transmission, cholinergic / intermediate filament / response to caffeine / blood circulation / eating behavior / inhibitory postsynaptic potential / alpha-actinin binding / regulation of calcium ion transport / presynaptic active zone / axolemma / asymmetric synapse / membrane depolarization / phagocytosis / prepulse inhibition / cellular defense response / neuron projection morphogenesis / regulation of mitochondrial membrane potential / presynaptic modulation of chemical synaptic transmission / response to amphetamine / positive regulation of synaptic transmission, glutamatergic / positive regulation of apoptotic signaling pathway / central nervous system development / positive regulation of long-term synaptic potentiation / excitatory postsynaptic potential / positive regulation of synaptic transmission, GABAergic / positive regulation of protein secretion / synaptic transmission, glutamatergic / astrocyte activation / locomotory behavior / apoptotic signaling pathway / electron transport chain / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / negative regulation of inflammatory response / adenylate cyclase-activating G protein-coupled receptor signaling pathway / blood coagulation / vasodilation / 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 / electron transfer activity / positive regulation of ERK1 and ERK2 cascade / calmodulin binding / inflammatory response / iron ion binding / response to xenobiotic stimulus / negative regulation of cell population proliferation / neuronal cell body / apoptotic process / lipid binding / heme binding / dendrite / 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 / Serpentine type 7TM GPCR chemoreceptor Srsx / Four Helix Bundle (Hemerythrin (Met), subunit A) / 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 / Serpentine type 7TM GPCR chemoreceptor Srsx / Four Helix Bundle (Hemerythrin (Met), subunit A) / 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 / SYNCHROTRON / SAD / Resolution: 2.14 Å
AuthorsWeinert, T. / Cheng, R. / James, D. / Gashi, D. / Nogly, P. / Jaeger, K. / Dore, A.S. / Geng, T. / Cooke, R. / 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 1.1Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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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)50,3649
Polymers47,9971
Non-polymers2,3688
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint10 kcal/mol
Surface area19730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.330, 180.070, 142.660
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, 41 molecules

#2: Chemical ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 3 / 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 / Comment: antagonist*YM
#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.: 33 / 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
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
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.14→34.5 Å / Num. obs: 30837 / % possible obs: 99.4 % / Redundancy: 1007.4 % / CC1/2: 0.99 / R split: 0.0466 / Net I/σ(I): 13.17
Reflection shellResolution: 2.14→2.22 Å / Redundancy: 8.1 % / Num. unique obs: 2842 / CC1/2: 0.12 / R split: 2.1176 / % possible all: 93.83

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
CrystFELdata reduction
CrystFELdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.14→34.458 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2292 1430 4.9 %
Rwork0.1989 --
obs0.2 29173 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.14→34.458 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2845 0 163 33 3041
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133143
X-RAY DIFFRACTIONf_angle_d1.1574320
X-RAY DIFFRACTIONf_dihedral_angle_d14.0611906
X-RAY DIFFRACTIONf_chiral_restr0.062528
X-RAY DIFFRACTIONf_plane_restr0.009551
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.14-2.21650.43081340.34962627X-RAY DIFFRACTION96
2.2165-2.30520.33041500.27382725X-RAY DIFFRACTION100
2.3052-2.41010.27631400.24012721X-RAY DIFFRACTION99
2.4101-2.53710.23791460.1852762X-RAY DIFFRACTION100
2.5371-2.6960.21871600.15652752X-RAY DIFFRACTION100
2.696-2.90410.20481380.15562767X-RAY DIFFRACTION100
2.9041-3.19620.20121450.16282767X-RAY DIFFRACTION100
3.1962-3.65820.23461540.16482801X-RAY DIFFRACTION100
3.6582-4.60720.20671300.17842841X-RAY DIFFRACTION100
4.6072-34.46270.21531330.2172980X-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)
12.07770.43020.66891.5413-0.24573.4282-0.02640.05560.0503-0.05780.0272-0.1251-0.06610.2933-0.00760.38230.00490.04940.3907-0.03080.27226.37286.355250.4967
2-0.01050.5579-0.05372.3797-0.2119-0.13610.053-0.0161-0.65760.6360.26851.60920.4819-0.2194-0.25841.1404-0.1513-0.00320.73280.02241.6112-20.405242.716750.5311
33.547-0.22851.13741.10581.27742.99050.0452-0.2647-0.52390.47470.19940.13710.6166-0.19260.13650.5451-0.09870.08410.40680.0160.3418-3.294477.748959.1841
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 318 )
3X-RAY DIFFRACTION3chain 'A' and (resid 319 through 409 )

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