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- PDB-2y02: TURKEY BETA1 ADRENERGIC RECEPTOR WITH STABILISING MUTATIONS AND B... -

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Basic information

Entry
Database: PDB / ID: 2y02
TitleTURKEY BETA1 ADRENERGIC RECEPTOR WITH STABILISING MUTATIONS AND BOUND AGONIST CARMOTEROL
ComponentsBETA-1 ADRENERGIC RECEPTOR
KeywordsRECEPTOR / G PROTEIN COUPLED RECEPTOR / SEVEN-HELIX RECEPTOR / INTEGRAL MEMBRANE PROTEIN / THERMOSTABILISING POINT MUTATIONS / GPCR
Function / homologyG protein-coupled receptor, rhodopsin-like / G-protein coupled receptors family 1 profile. / G-protein coupled receptors family 1 signature. / 7 transmembrane receptor (rhodopsin family) / GPCR, rhodopsin-like, 7TM / Adrenoceptor family / Beta 1 adrenoceptor / beta1-adrenergic receptor activity / positive regulation of heart contraction / adenylate cyclase-activating adrenergic receptor signaling pathway ...G protein-coupled receptor, rhodopsin-like / G-protein coupled receptors family 1 profile. / G-protein coupled receptors family 1 signature. / 7 transmembrane receptor (rhodopsin family) / GPCR, rhodopsin-like, 7TM / Adrenoceptor family / Beta 1 adrenoceptor / beta1-adrenergic receptor activity / positive regulation of heart contraction / adenylate cyclase-activating adrenergic receptor signaling pathway / sodium ion binding / positive regulation of GTPase activity / Ras guanyl-nucleotide exchange factor activity / drug binding / early endosome / integral component of plasma membrane / membrane / identical protein binding / plasma membrane / Beta-1 adrenergic receptor
Function and homology information
Specimen sourceMELEAGRIS GALLOPAVO (turkey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 2.6 Å resolution
AuthorsWarne, A. / Moukhametzianov, R. / Baker, J.G. / Nehme, R. / Edwards, P.C. / Leslie, A.G.W. / Schertler, G.F.X. / Tate, C.G.
Citation
Journal: Nature / Year: 2011
Title: The Structural Basis for Agonist and Partial Agonist Action on a Beta1-Adrenergic Receptor
Authors: Warne, A. / Moukhametzianov, R. / Baker, J.G. / Nehme, R. / Edwards, P.C. / Leslie, A.G.W. / Schertler, G.F.X. / Tate, C.G.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2008
Title: Conformational Thermostabilization of the Beta1-Adrenergic Receptor in a Detergent-Resistant Form.
Authors: Serrano-Vega, M.J. / Magnani, F. / Shibata, Y. / Tate, C.G.
#2: Journal: Nature / Year: 2008
Title: Structure of a Beta1-Adrenergic G-Protein-Coupled Receptor.
Authors: Warne, T. / Serrano-Vega, M.J. / Baker, J.G. / Moukhametzianov, R. / Edwards, P.C. / Henderson, R. / Leslie, A.G.W. / Tate, C.G. / Schertler, G.F.X.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 30, 2010 / Release: Jan 12, 2011
RevisionDateData content typeGroupProviderType
1.0Jan 12, 2011Structure modelrepositoryInitial release
1.1Sep 25, 2013Structure modelDerived calculations / Structure summary / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BETA-1 ADRENERGIC RECEPTOR
B: BETA-1 ADRENERGIC RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,38319
Polyers71,8822
Non-polymers6,50217
Water72140
1
A: BETA-1 ADRENERGIC RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,20310
Polyers35,9411
Non-polymers3,2629
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: BETA-1 ADRENERGIC RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1809
Polyers35,9411
Non-polymers3,2398
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)8580
ΔGint (kcal/M)-40.5
Surface area (Å2)29340
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)89.600, 61.700, 101.400
Angle α, β, γ (deg.)90.00, 109.30, 90.00
Int Tables number4
Space group name H-MP 1 21 1

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Components

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Protein/peptide , 1 types, 2 molecules AB

#1: Protein/peptide BETA-1 ADRENERGIC RECEPTOR / / BETA-1 ADRENORECEPTOR / BETA-1 ADRENOCEPTOR / BETA-T


Mass: 35940.777 Da / Num. of mol.: 2
Details: RESIDUES 3-32 AT THE N-TERMINUS AND RESIDUES 244-271 OF THE THIRD INTRACELLULAR LOOP WERE DELETED ...RESIDUES 3-32 AT THE N-TERMINUS AND RESIDUES 244-271 OF THE THIRD INTRACELLULAR LOOP WERE DELETED FROM THE CONSTRUCT. THE CONSTRUCT WAS TRUNCATED AFTER RESIDUE 367 AND A HEXAHIS TAG ADDED.
Fragment: RESIDUES 33-368 / Mutation: YES / Source: (gene. exp.) MELEAGRIS GALLOPAVO (turkey) / Cell: ERYTHROCYTERed blood cell / Plasmid name: PBACPAK8 / Cell line (production host): HIGH FIVE / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: P07700

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Non-polymers , 5 types, 57 molecules

#2: Chemical
ChemComp-Y01 / CHOLESTEROL HEMISUCCINATE


Mass: 486.726 Da / Num. of mol.: 4 / Formula: C31H50O4
#3: Chemical
ChemComp-2CV / HEGA-10


Mass: 379.489 Da / Num. of mol.: 10 / Formula: C18H37NO7 / Comment: detergent *YM
#4: Chemical ChemComp-WHJ / CARMOTEROL


Mass: 368.426 Da / Num. of mol.: 2 / Formula: C21H24N2O4 / Carmoterol
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Formula: Na / Sodium
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / Formula: H2O / Water

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Details

Sequence detailsTHE FOLLOWING MUTATIONS WERE MADE TO IMPROVE THERMOSTABILITY R68S,M90V,Y227A,A282L,F327A,F338M THE ...THE FOLLOWING MUTATIONS WERE MADE TO IMPROVE THERMOSTABILITY R68S,M90V,Y227A,A282L,F327A,F338M THE FOLLOWING MUTATIONS WERE MADE TO IMPROVE EXPRESSION AND HELP CRYSTALLISATION C116L, C358A

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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: 3.78 / Density percent sol: 67 % / Description: NONE
Crystal growpH: 9
Details: SITTING DROP VAPOUR DIFFUSION, PROTEIN (16MG/ML) IN 100MM NACL, 0.1MM EDTA, 1.0MM (R, R)-CARMOTEROL, 1.9MG/ML CHS, 0.65% HEGA-10, 0.1M BICINE PH9.0, 26% PEG600 AT 4 DEGREES C

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARRESEARCH / Detector: CCD / Collection date: Oct 3, 2009
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 42.2 Å2 / D resolution high: 2.6 Å / D resolution low: 42.3 Å / Number obs: 31463 / Observed criterion sigma I: 0 / Rmerge I obs: 0.13 / NetI over sigmaI: 7.5 / Redundancy: 3.2 % / Percent possible obs: 97.1
Reflection shellRmerge I obs: 0.6 / Highest resolution: 2.6 Å / Lowest resolution: 2.74 Å / MeanI over sigI obs: 1.9 / Redundancy: 2.8 % / Percent possible all: 93.6

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VT4
Correlation coeff Fo to Fc: 0.906 / Correlation coeff Fo to Fc free: 0.874 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. / Overall SU B: 9.518 / Overall SU ML: 0.203 / R Free selection details: RANDOM / Cross valid method: THROUGHOUT / Overall ESU R: 0.446 / Overall ESU R Free: 0.296 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Solvent computationSolvent ion probe radii: 0.8 Å / Solvent shrinkage radii: 0.8 Å / Solvent vdw probe radii: 1.4 Å / Solvent model details: MASK
Displacement parametersB iso mean: 37.453 Å2 / Aniso B11: 0.17 Å2 / Aniso B12: 0 Å2 / Aniso B13: 0.71 Å2 / Aniso B22: 1.61 Å2 / Aniso B23: 0 Å2 / Aniso B33: -1.32 Å2
Least-squares processR factor R free: 0.26828 / R factor R work: 0.22946 / R factor obs: 0.23142 / Highest resolution: 2.6 Å / Lowest resolution: 95.73 Å / Number reflection R free: 1602 / Number reflection obs: 29861 / Percent reflection R free: 5.1 / Percent reflection obs: 96.72
Refine hist #LASTHighest resolution: 2.6 Å / Lowest resolution: 95.73 Å
Number of atoms included #LASTProtein: 4640 / Nucleic acid: 0 / Ligand: 384 / Solvent: 40 / Total: 5064
Refine LS restraints
Refine IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0225145
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3912.0196990
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8025.000581
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.69422.022178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.16315.000808
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.84415.00035
X-RAY DIFFRACTIONr_chiral_restr0.0900.200835
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213585
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.5143.0002918
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.8395.0004733
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.5935.0002227
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.94810.0002257
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints ncs

Ens ID: 1 / Refine ID: X-RAY DIFFRACTION

Dom IDAuth asym IDNumberTypeRms dev positionWeight position
1A1327tight positional0.040.05
2B1327tight positional0.040.05
1A208medium positional0.060.50
2B208medium positional0.060.50
1A1327tight thermal3.8710.00
2B1327tight thermal3.8710.00
1A208medium thermal3.0520.00
2B208medium thermal3.0520.00
Refine LS shellHighest resolution: 2.6 Å / R factor R free: 0.372 / R factor R work: 0.329 / Lowest resolution: 2.668 Å / Number reflection R free: 104 / Number reflection R work: 2100 / Total number of bins used: 20 / Percent reflection obs: 92.53

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