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- PDB-6mh8: High-viscosity injector-based Pink Beam Serial Crystallography of... -

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Basic information

Entry
Database: PDB / ID: 6mh8
TitleHigh-viscosity injector-based Pink Beam Serial Crystallography of Micro-crystals at a Synchrotron Radiation Source
ComponentsAdenosine receptor A2a, Soluble cytochrome b562 chimeric construct
KeywordsMEMBRANE PROTEIN / GPCR / Pink beam serial crystallography
Function / homology
Function and homology information


regulation of norepinephrine secretion / positive regulation of circadian sleep/wake cycle, sleep / Adenosine P1 receptors / positive regulation of acetylcholine secretion, neurotransmission / G protein-coupled adenosine receptor activity / response to purine-containing compound / G protein-coupled adenosine receptor signaling pathway / NGF-independant TRKA activation / Surfactant metabolism / type 5 metabotropic glutamate receptor binding ...regulation of norepinephrine secretion / positive regulation of circadian sleep/wake cycle, sleep / Adenosine P1 receptors / positive regulation of acetylcholine secretion, neurotransmission / G protein-coupled adenosine receptor activity / response to purine-containing compound / G protein-coupled adenosine receptor signaling pathway / NGF-independant TRKA activation / Surfactant metabolism / type 5 metabotropic glutamate receptor binding / negative regulation of vascular permeability / positive regulation of urine volume / intermediate filament / response to caffeine / blood circulation / presynaptic active zone / synaptic transmission, cholinergic / sensory perception / eating behavior / positive regulation of glutamate secretion / regulation of calcium ion transport / alpha-actinin binding / synaptic transmission, dopaminergic / membrane depolarization / asymmetric synapse / axolemma / prepulse inhibition / cellular defense response / phagocytosis / neuron projection morphogenesis / positive regulation of synaptic transmission, glutamatergic / presynaptic modulation of chemical synaptic transmission / astrocyte activation / regulation of mitochondrial membrane potential / excitatory postsynaptic potential / positive regulation of protein secretion / locomotory behavior / positive regulation of long-term synaptic potentiation / central nervous system development / electron transport chain / synaptic transmission, glutamatergic / vasodilation / blood coagulation / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / phospholipase C-activating G protein-coupled receptor signaling pathway / cell-cell signaling / adenylate cyclase-activating G protein-coupled receptor signaling pathway / presynaptic membrane / negative regulation of neuron apoptotic process / G alpha (s) signalling events / positive regulation of ERK1 and ERK2 cascade / calmodulin binding / electron transfer activity / periplasmic space / postsynaptic membrane / response to xenobiotic stimulus / iron ion binding / inflammatory response / negative regulation of cell population proliferation / neuronal cell body / heme binding / apoptotic process / regulation of DNA-templated transcription / lipid binding / dendrite / protein-containing complex binding / glutamatergic synapse / 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. / 7 transmembrane receptor (rhodopsin family) / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile.
Similarity search - Domain/homology
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: 4.2 Å
AuthorsMartin-Garcia, J.M. / Zhu, L. / Mendez, D. / Lee, M. / Chun, E. / Li, C. / Hu, H. / Subramanian, G. / Kissick, D. / Ogata, C. ...Martin-Garcia, J.M. / Zhu, L. / Mendez, D. / Lee, M. / Chun, E. / Li, C. / Hu, H. / Subramanian, G. / Kissick, D. / Ogata, C. / Henning, R. / Ishchenko, A. / Dobson, Z. / Zhan, S. / Weierstall, U. / Spence, J.C.H. / Fromme, P. / Zatsepin, N.A. / Fischetti, R.F. / Cherezov, V. / Liu, W.
Funding support United States, 10items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1231306 United States
National Science Foundation (NSF, United States)1565180 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R21DA042298 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM124152 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)R35GM127086 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R24GM111072 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)ACB-12002 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)AGM12006 United States
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
CitationJournal: Iucrj / Year: 2019
Title: High-viscosity injector-based pink-beam serial crystallography of microcrystals at a synchrotron radiation source.
Authors: Martin-Garcia, J.M. / Zhu, L. / Mendez, D. / Lee, M.Y. / Chun, E. / Li, C. / Hu, H. / Subramanian, G. / Kissick, D. / Ogata, C. / Henning, R. / Ishchenko, A. / Dobson, Z. / Zhang, S. / ...Authors: Martin-Garcia, J.M. / Zhu, L. / Mendez, D. / Lee, M.Y. / Chun, E. / Li, C. / Hu, H. / Subramanian, G. / Kissick, D. / Ogata, C. / Henning, R. / Ishchenko, A. / Dobson, Z. / Zhang, S. / Weierstall, U. / Spence, J.C.H. / Fromme, P. / Zatsepin, N.A. / Fischetti, R.F. / Cherezov, V. / Liu, W.
History
DepositionSep 17, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1May 29, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Aug 21, 2019Group: Data collection / Category: reflns / reflns_shell / Item: _reflns.pdbx_R_split / _reflns_shell.pdbx_R_split
Revision 1.3Nov 6, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support
Revision 1.4Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 11, 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 1.6Nov 1, 2023Group: Refinement description / Category: software / Item: _software.name
Revision 1.7Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Adenosine receptor A2a, Soluble cytochrome b562 chimeric construct
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3122
Polymers49,9741
Non-polymers3371
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area19790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.000, 179.000, 142.000
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 chimeric construct / 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


Mass: 337.336 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H15N7O2 / Comment: antagonist*YM
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: 2.54 Å3/Da / Density % sol: 51.63 %
Crystal growTemperature: 298 K / Method: lipidic cubic phase / pH: 5 / Details: sodium citrate pH 5.0, PEG 400, sodium thiocyanate

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 1.033-1.67
DetectorType: RAYONIX MX340-HS / Detector: CCD / Date: Jun 24, 2017
RadiationProtocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.0331
21.671
ReflectionResolution: 4.2→50 Å / Num. obs: 4021 / % possible obs: 87.8 % / Redundancy: 11.5 % / R split: 0.27 / Net I/σ(I): 4.5
Reflection shellResolution: 4.2→4.3 Å / R split: 0.262

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
CrystFELdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UVI

5uvi


Resolution: 4.2→50 Å / Cor.coef. Fo:Fc: 0.841 / Cor.coef. Fo:Fc free: 0.798 / SU B: 84.914 / SU ML: 1.114 / Cross valid method: THROUGHOUT / ESU R Free: 1.27 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28767 353 10 %RANDOM
Rwork0.24997 ---
obs0.25385 3179 87.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 58.074 Å2
Baniso -1Baniso -2Baniso -3
1--0.74 Å2-0 Å2-0 Å2
2--0.82 Å2-0 Å2
3----0.08 Å2
Refinement stepCycle: 1 / Resolution: 4.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2978 0 25 0 3003
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0193073
X-RAY DIFFRACTIONr_bond_other_d0.0020.022985
X-RAY DIFFRACTIONr_angle_refined_deg1.0431.9584192
X-RAY DIFFRACTIONr_angle_other_deg0.86136789
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0735387
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.51823.675117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.45815475
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1281513
X-RAY DIFFRACTIONr_chiral_restr0.0450.2499
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023466
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02731
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_it2.4025.9511560
X-RAY DIFFRACTIONr_mcbond_other2.3825.9461559
X-RAY DIFFRACTIONr_mcangle_it4.2228.9061943
X-RAY DIFFRACTIONr_mcangle_other4.2238.9111944
X-RAY DIFFRACTIONr_scbond_it1.8535.9221513
X-RAY DIFFRACTIONr_scbond_other1.8525.9211514
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.478.822250
X-RAY DIFFRACTIONr_long_range_B_refined11.52254.85413268
X-RAY DIFFRACTIONr_long_range_B_other11.52254.85313269
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 4.2→4.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 22 -
Rwork0.208 209 -
obs--78.84 %

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