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- PDB-5n2s: Crystal structure of stabilized A1 receptor in complex with PSB36... -

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Basic information

Entry
Database: PDB / ID: 5n2s
TitleCrystal structure of stabilized A1 receptor in complex with PSB36 at 3.3A resolution
ComponentsSoluble cytochrome b562,Adenosine receptor A1
KeywordsMEMBRANE PROTEIN / G-PROTEIN-COUPLED RECEPTOR / INTEGRAL THERMOSTABILIZING MUTATIONS
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 / positive regulation of lipid catabolic process ...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 / positive regulation of lipid catabolic process / negative regulation of synaptic transmission, GABAergic / negative regulation of hormone secretion / Adenosine P1 receptors / mucus secretion / regulation of respiratory gaseous exchange by nervous system process / negative regulation of leukocyte migration / heterotrimeric G-protein binding / regulation of sensory perception of pain / G protein-coupled adenosine receptor activity / regulation of presynaptic cytosolic calcium ion concentration / positive regulation of systemic arterial blood pressure / response to purine-containing compound / 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 / leukocyte migration / temperature homeostasis / negative regulation of acute inflammatory response / presynaptic active zone / detection of temperature stimulus involved in sensory perception of pain / calyx of Held / negative regulation of long-term synaptic potentiation / asymmetric synapse / axolemma / fatty acid homeostasis / negative regulation of lipid catabolic process / phagocytosis / lipid catabolic process / : / heat shock protein binding / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / excitatory postsynaptic potential / apoptotic signaling pathway / G protein-coupled receptor binding / 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 / protein heterodimerization activity / G protein-coupled receptor signaling pathway / negative regulation of cell population proliferation / neuronal cell body / dendrite / heme binding / synapse / negative regulation of apoptotic process / signal transduction / plasma membrane
Similarity search - Function
Adenosine A1 receptor / Adenosine receptor / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / 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 ...Adenosine A1 receptor / Adenosine receptor / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / 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) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-8K8 / Soluble cytochrome b562 / Adenosine receptor A1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.303 Å
AuthorsCheng, R.K.Y. / Segala, E. / Robertson, N. / Deflorian, F. / Dore, A.S. / Errey, J.C. / Fiez-Vandal, C. / Marshall, F.H. / Cooke, R.M.
CitationJournal: Structure / Year: 2017
Title: Structures of Human A1 and A2A Adenosine Receptors with Xanthines Reveal Determinants of Selectivity.
Authors: Cheng, R.K.Y. / Segala, E. / Robertson, N. / Deflorian, F. / Dore, A.S. / Errey, J.C. / Fiez-Vandal, C. / Marshall, F.H. / Cooke, R.M.
History
DepositionFeb 8, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 26, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)49,0244
Polymers48,4461
Non-polymers5793
Water362
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-15 kcal/mol
Surface area21230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.273, 111.658, 160.543
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-1329-

LYS

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Components

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


Mass: 48445.855 Da / Num. of mol.: 1
Mutation: A57L, T91A, N159A, Y205A, L236A, L240A, T277A, C309S,A57L, T91A, N159A, Y205A, L236A, L240A, T277A, C309S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Homo sapiens (human)
Gene: cybC, ADORA1 / Plasmid: PFAST-BAC / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): TNI PRO / References: UniProt: P0ABE7, UniProt: P30542
#2: Chemical ChemComp-8K8 / 1-butyl-3-(3-oxidanylpropyl)-8-[(1~{R},5~{S})-3-tricyclo[3.3.1.0^{3,7}]nonanyl]-7~{H}-purine-2,6-dione


Mass: 386.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N4O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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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: 3.72 Å3/Da / Density % sol: 66.92 % / Description: PLATES
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 7.5
Details: 0.1M SODIUM / POTASSIUM PHOSPHATE PH 7.5, 0.2M LITHIUM SULPHATE, 37.5% (W/V) PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96863 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 30, 2016 / Details: (DOUBLE) KB MIRROR PAIR
RadiationMonochromator: DOUBLE SI(111) CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96863 Å / Relative weight: 1
ReflectionResolution: 3.303→160.6 Å / Num. obs: 9824 / % possible obs: 97.8 % / Redundancy: 5.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.137 / Net I/σ(I): 7.9
Reflection shellResolution: 3.303→3.57 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.887 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1930 / CC1/2: 0.782 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSJanuary, 2014data reduction
Aimless0.5.9data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IU4

5iu4


Resolution: 3.303→32.891 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.76
RfactorNum. reflection% reflection
Rfree0.2784 459 4.81 %
Rwork0.256 --
obs0.2571 9534 97.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.303→32.891 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2989 0 38 2 3029
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023096
X-RAY DIFFRACTIONf_angle_d0.5174218
X-RAY DIFFRACTIONf_dihedral_angle_d14.4361123
X-RAY DIFFRACTIONf_chiral_restr0.036498
X-RAY DIFFRACTIONf_plane_restr0.004513
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3032-3.78060.3681480.32212987X-RAY DIFFRACTION98
3.7806-4.76080.28671570.24373010X-RAY DIFFRACTION98
4.7608-32.89250.24211540.24083078X-RAY DIFFRACTION96
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)
13.27070.3885-1.07053.7243-0.60151.2605-0.24820.4139-0.0339-0.1923-0.09350.0265-0.3154-0.74240.31270.98050.0962-0.06140.5931-0.02730.400997.3926127.228830.0811
22.89110.9512-1.95065.2813-1.34375.2519-0.0141-0.04610.0864-0.1369-0.1384-0.55-1.05650.19610.12470.6657-0.0067-0.06350.465-0.07570.4964107.6226127.752236.655
33.19990.3987-3.7121.2448-0.58346.79470.0542-0.7537-0.6426-0.1255-0.3897-0.28120.16191.86160.4231.42920.06810.11491.65370.09060.800584.4289151.735480.2163
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 6:139)
2X-RAY DIFFRACTION2(chain A and resid 140:295)
3X-RAY DIFFRACTION3(chain A and resid 1002:1104)

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