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- PDB-5uen: Crystal structure of the human adenosine A1 receptor A1AR-bRIL in... -

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Basic information

Entry
Database: PDB / ID: 5uen
TitleCrystal structure of the human adenosine A1 receptor A1AR-bRIL in complex with the covalent antagonist DU172 at 3.2A resolution
ComponentsAdenosine receptor A1,Soluble cytochrome b562,Adenosine receptor A1
KeywordsMEMBRANE PROTEIN / GPCR / transmembrane / receptor / adenosine
Function / homology
Function and homology information


positive regulation of nucleoside transport / negative regulation of neurotrophin production / regulation of glomerular filtration / negative regulation of circadian sleep/wake cycle, non-REM sleep / positive regulation of peptide secretion / negative regulation of mucus secretion / purine nucleoside binding / negative regulation of glutamate secretion / negative regulation of long-term synaptic depression / negative regulation of hormone secretion ...positive regulation of nucleoside transport / negative regulation of neurotrophin production / regulation of glomerular filtration / negative regulation of circadian sleep/wake cycle, non-REM sleep / positive regulation of peptide secretion / negative regulation of mucus secretion / purine nucleoside binding / negative regulation of glutamate secretion / negative regulation of long-term synaptic depression / negative regulation of hormone secretion / positive regulation of lipid catabolic process / negative regulation of synaptic transmission, GABAergic / heterotrimeric G-protein binding / Adenosine P1 receptors / mucus secretion / G protein-coupled adenosine receptor activity / regulation of respiratory gaseous exchange by nervous system process / negative regulation of leukocyte migration / regulation of presynaptic cytosolic calcium ion concentration / regulation of sensory perception of pain / response to purine-containing compound / positive regulation of systemic arterial blood pressure / positive regulation of potassium ion transport / negative regulation of synaptic transmission, glutamatergic / negative regulation of systemic arterial blood pressure / regulation of cardiac muscle cell contraction / triglyceride homeostasis / protein targeting to membrane / long-term synaptic depression / temperature homeostasis / leukocyte migration / presynaptic active zone / calyx of Held / detection of temperature stimulus involved in sensory perception of pain / negative regulation of acute inflammatory response / negative regulation of long-term synaptic potentiation / asymmetric synapse / axolemma / : / fatty acid homeostasis / negative regulation of lipid catabolic process / phagocytosis / lipid catabolic process / positive regulation of protein dephosphorylation / heat shock protein binding / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / excitatory postsynaptic potential / G protein-coupled receptor binding / apoptotic signaling pathway / electron transport chain / G-protein beta/gamma-subunit complex binding / terminal bouton / cognition / vasodilation / cell-cell signaling / presynaptic membrane / nervous system development / G alpha (i) signalling events / basolateral plasma membrane / postsynaptic membrane / positive regulation of MAPK cascade / dendritic spine / periplasmic space / electron transfer activity / response to hypoxia / inflammatory response / iron ion binding / G protein-coupled receptor signaling pathway / protein heterodimerization activity / negative regulation of cell population proliferation / neuronal cell body / synapse / dendrite / heme binding / negative regulation of apoptotic process / signal transduction / plasma membrane
Similarity search - Function
Adenosine A1 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
Chem-DU1 / OLEIC ACID / Soluble cytochrome b562 / Adenosine receptor A1
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.2 Å
AuthorsGlukhova, A. / Thal, D.M. / Nguyen, A.T. / Vecchio, E.A. / Jorg, M. / Scammells, P.J. / May, L.T. / Sexton, P.M. / Christopoulos, A.
Funding support Australia, 2items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP10552134 Australia
National Health and Medical Research Council (NHMRC, Australia)APP1084246 Australia
CitationJournal: Cell / Year: 2017
Title: Structure of the Adenosine A1 Receptor Reveals the Basis for Subtype Selectivity.
Authors: Glukhova, A. / Thal, D.M. / Nguyen, A.T. / Vecchio, E.A. / Jorg, M. / Scammells, P.J. / May, L.T. / Sexton, P.M. / Christopoulos, A.
History
DepositionJan 3, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2017Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Data collection / Category: diffrn_source / pdbx_audit_support
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Adenosine receptor A1,Soluble cytochrome b562,Adenosine receptor A1
B: Adenosine receptor A1,Soluble cytochrome b562,Adenosine receptor A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,13611
Polymers93,1202
Non-polymers3,0169
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.492, 112.960, 124.171
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Adenosine receptor A1,Soluble cytochrome b562,Adenosine receptor A1 / Cytochrome b-562


Mass: 46560.031 Da / Num. of mol.: 2
Fragment: UNP P30542 reisues 2-210, UNP P0ABE7 residues 23-127, UNP P30542 residues 228-31,UNP P30542 reisues 2-210, UNP P0ABE7 residues 23-127, UNP P30542 residues 228-31,UNP P30542 reisues 2-210, ...Fragment: UNP P30542 reisues 2-210, UNP P0ABE7 residues 23-127, UNP P30542 residues 228-31,UNP P30542 reisues 2-210, UNP P0ABE7 residues 23-127, UNP P30542 residues 228-31,UNP P30542 reisues 2-210, UNP P0ABE7 residues 23-127, UNP P30542 residues 228-31
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Escherichia coli (E. coli)
Gene: ADORA1, cybC / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P30542, UniProt: P0ABE7
#2: Chemical ChemComp-DU1 / 4-{[3-(8-cyclohexyl-2,6-dioxo-1-propyl-1,2,6,7-tetrahydro-3H-purin-3-yl)propyl]carbamoyl}benzene-1-sulfonyl fluoride


Mass: 519.589 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H30FN5O5S
#3: Chemical
ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 7 / 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: 3.63 Å3/Da / Density % sol: 66.15 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 100 mM Hepes pH 7.0-8.0, 28-38% PEG 300 and 500-700 mM NH4F
PH range: 7.0-8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 24, 2016
RadiationMonochromator: Silicon Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3.2→30 Å / Num. obs: 23000 / % possible obs: 99.8 % / Redundancy: 14.1 % / Rmerge(I) obs: 0.328 / Net I/σ(I): 12.6
Reflection shellResolution: 3.2→3.42 Å / Redundancy: 14.4 % / Rmerge(I) obs: 2.767 / Num. unique obs: 4121 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.51 Å29.52 Å
Translation6.51 Å29.52 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
Aimless0.5.15data scaling
PHASER2.5.6phasing
Coot0.8.6model building
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EIY

4eiy


Resolution: 3.2→30 Å / SU B: 59.391 / SU ML: 0.482 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.553
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.316 1105 4.8 %RANDOM
Rwork0.286 ---
obs0.288 21759 99.2 %-
Displacement parametersBiso max: 235.06 Å2 / Biso mean: 92.83 Å2 / Biso min: 50.16 Å2
Baniso -1Baniso -2Baniso -3
1--6.32 Å20 Å20 Å2
2--6.09 Å20 Å2
3---0.23 Å2
Refinement stepCycle: final / Resolution: 3.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6061 0 189 0 6250
Biso mean--74.41 --
Num. residues----767
Refine LS restraints
Refine-IDType
X-RAY DIFFRACTIONBOND LENGTH (A)
X-RAY DIFFRACTIONANGLE DISTANCE (A)
X-RAY DIFFRACTIONINTRAPLANAR 1-4 DISTANCE (A)
X-RAY DIFFRACTIONH-BOND OR METAL COORDINATION (A)
X-RAY DIFFRACTIONMAIN-CHAIN BOND (A**2)
X-RAY DIFFRACTIONMAIN-CHAIN ANGLE (A**2)
X-RAY DIFFRACTIONSIDE-CHAIN BOND (A**2)
X-RAY DIFFRACTIONSIDE-CHAIN ANGLE (A**2)
LS refinement shellResolution: 3.2→3.282 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.424 69 -
Rwork0.366 1598 -
obs--99.17 %

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