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Entry
Database: PDB / ID: 5uvi
TitleSerial Millisecond Crystallography of Membrane and Soluble Protein Micro-crystals using Synchrotron Radiation
ComponentsAdenosine receptor A2a,Soluble cytochrome b562,Adenosine receptor A2a
KeywordsMEMBRANE PROTEIN / GPCR
Function / homology
Function and homology information


positive regulation of acetylcholine secretion, neurotransmission / positive regulation of circadian sleep/wake cycle, sleep / regulation of norepinephrine secretion / negative regulation of alpha-beta T cell activation / Adenosine P1 receptors / 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 / positive regulation of circadian sleep/wake cycle, sleep / regulation of norepinephrine secretion / negative regulation of alpha-beta T cell activation / Adenosine P1 receptors / 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 / locomotory behavior / regulation of mitochondrial membrane potential / synaptic transmission, glutamatergic / central nervous system development / positive regulation of long-term synaptic potentiation / astrocyte activation / apoptotic signaling pathway / positive regulation of protein secretion / positive regulation of synaptic transmission, GABAergic / 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 / 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: 3.2 Å
AuthorsMartin-Garcia, J.M. / Conrad, C.E. / Nelson, G. / Stander, N. / Zatsepin, N.A. / Zook, J. / Zhu, L. / Geiger, J. / Chun, E. / Kissick, D. ...Martin-Garcia, J.M. / Conrad, C.E. / Nelson, G. / Stander, N. / Zatsepin, N.A. / Zook, J. / Zhu, L. / Geiger, J. / Chun, E. / Kissick, D. / Hilgart, M.C. / Ogata, C. / Ishchenko, A. / Nagaratnam, N. / Roy-Chowdhury, S. / Coe, J. / Subramanian, G. / Schaffer, A. / James, D. / Ketawala, G. / Venugopalan, N. / Xu, S. / Corcoran, S. / Ferguson, D. / Weierstall, U. / Spence, J.C.H. / Cherezov, V. / Fromme, P. / Fischetti, R.F. / Liu, W.
Funding support United States, 8items
OrganizationGrant numberCountry
Flinn Foundation1991 United States
STC Program of the National Science Foundation through BioXFEL1231306 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM095583 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM108635 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U54GM094618 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)Y1-CO-1020 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)Y1-GM-1104 United States
Department of Energy (DOE, United States)DE-AC02-06CH1135 United States
CitationJournal: IUCrJ / Year: 2017
Title: Serial millisecond crystallography of membrane and soluble protein microcrystals using synchrotron radiation.
Authors: Martin-Garcia, J.M. / Conrad, C.E. / Nelson, G. / Stander, N. / Zatsepin, N.A. / Zook, J. / Zhu, L. / Geiger, J. / Chun, E. / Kissick, D. / Hilgart, M.C. / Ogata, C. / Ishchenko, A. / ...Authors: Martin-Garcia, J.M. / Conrad, C.E. / Nelson, G. / Stander, N. / Zatsepin, N.A. / Zook, J. / Zhu, L. / Geiger, J. / Chun, E. / Kissick, D. / Hilgart, M.C. / Ogata, C. / Ishchenko, A. / Nagaratnam, N. / Roy-Chowdhury, S. / Coe, J. / Subramanian, G. / Schaffer, A. / James, D. / Ketwala, G. / Venugopalan, N. / Xu, S. / Corcoran, S. / Ferguson, D. / Weierstall, U. / Spence, J.C.H. / Cherezov, V. / Fromme, P. / Fischetti, R.F. / Liu, W.
History
DepositionFeb 20, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.year
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Apr 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Apr 13, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.6Oct 4, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)52,4678
Polymers49,9741
Non-polymers2,4937
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.300, 180.300, 142.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Adenosine receptor A2a,Soluble cytochrome b562,Adenosine receptor A2a / Cytochrome b-562


Mass: 49974.281 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: Spodoptera frugiperda (fall armyworm) / References: UniProt: P29274, UniProt: P0ABE7
#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-CLR / CHOLESTEROL / Cholesterol


Mass: 386.654 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C27H46O
#4: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H40O4
#5: Chemical ChemComp-OLA / OLEIC ACID / Oleic acid


Mass: 282.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H34O2

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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: 2.59 Å3/Da / Density % sol: 52.54 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 5
Details: 0.1 M sodium citrate pH 5.0, 32 % PEG 400, 75 mM sodium thocyanate

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 3.2→45 Å / Num. obs: 7702 / % possible obs: 99.8 % / Redundancy: 142.6 % / CC1/2: 0.992 / Net I/σ(I): 7.7
Reflection shellResolution: 3.2→3.28 Å / CC1/2: 0.423 / % possible all: 98.32

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
Cheetahdata collection
CrystFEL0.6.2data scaling
CrystFEL0.6.2data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5K2B

5k2b


Resolution: 3.2→45 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.914 / SU B: 44.863 / SU ML: 0.683 / Cross valid method: THROUGHOUT / ESU R Free: 0.619 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28721 1301 14.5 %RANDOM
Rwork0.24132 ---
obs0.24786 7702 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 107.47 Å2
Baniso -1Baniso -2Baniso -3
1-3.46 Å20 Å20 Å2
2---3.1 Å20 Å2
3----0.36 Å2
Refinement stepCycle: 1 / Resolution: 3.2→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2978 0 152 0 3130
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0193216
X-RAY DIFFRACTIONr_bond_other_d0.0030.023195
X-RAY DIFFRACTIONr_angle_refined_deg1.6142.0024388
X-RAY DIFFRACTIONr_angle_other_deg1.06837293
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6585387
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.89423.675117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.03415485
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5481513
X-RAY DIFFRACTIONr_chiral_restr0.0580.2528
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023503
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02739
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.72810.7861560
X-RAY DIFFRACTIONr_mcbond_other4.7210.7831559
X-RAY DIFFRACTIONr_mcangle_it7.71816.1711943
X-RAY DIFFRACTIONr_mcangle_other7.7216.1751944
X-RAY DIFFRACTIONr_scbond_it4.26611.1171652
X-RAY DIFFRACTIONr_scbond_other4.26511.1221653
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.17316.5652444
X-RAY DIFFRACTIONr_long_range_B_refined12.83413130
X-RAY DIFFRACTIONr_long_range_B_other12.82613130
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.2→3.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.394 89 -
Rwork0.396 555 -
obs--98.32 %

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