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- PDB-3ny9: Crystal structure of the human beta2 adrenergic receptor in compl... -

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Basic information

Entry
Database: PDB / ID: 3ny9
TitleCrystal structure of the human beta2 adrenergic receptor in complex with a novel inverse agonist
ComponentsBeta-2 adrenergic receptor, Lysozyme
KeywordsMEMBRANE PROTEIN / G Protein-coupled receptor / Lysozyme / Fusion / Transducer / Adrenergic / G-Proteins / Arrestins / Adrenalin / Compound 2 / Glycosylation / Palmitoylation / Phosphorylation / HYDROLASE / Structural Genomics / PSI-2 / Protein Structure Initiative / Accelerated Technologies Center for Gene to 3D Structure / ATCG3D / GPCR Network / GPCR
Function / homology
Function and homology information


beta2-adrenergic receptor activity / desensitization of G protein-coupled receptor signaling pathway by arrestin / positive regulation of mini excitatory postsynaptic potential / norepinephrine-epinephrine-mediated vasodilation involved in regulation of systemic arterial blood pressure / positive regulation of cAMP-dependent protein kinase activity / Adrenoceptors / norepinephrine binding / positive regulation of autophagosome maturation / heat generation / activation of transmembrane receptor protein tyrosine kinase activity ...beta2-adrenergic receptor activity / desensitization of G protein-coupled receptor signaling pathway by arrestin / positive regulation of mini excitatory postsynaptic potential / norepinephrine-epinephrine-mediated vasodilation involved in regulation of systemic arterial blood pressure / positive regulation of cAMP-dependent protein kinase activity / Adrenoceptors / norepinephrine binding / positive regulation of autophagosome maturation / heat generation / activation of transmembrane receptor protein tyrosine kinase activity / positive regulation of lipophagy / negative regulation of smooth muscle contraction / response to psychosocial stress / negative regulation of multicellular organism growth / positive regulation of AMPA receptor activity / adrenergic receptor signaling pathway / diet induced thermogenesis / endosome to lysosome transport / brown fat cell differentiation / adenylate cyclase-activating adrenergic receptor signaling pathway / positive regulation of protein kinase A signaling / potassium channel regulator activity / adenylate cyclase binding / positive regulation of bone mineralization / bone resorption / regulation of sodium ion transport / activation of adenylate cyclase activity / receptor-mediated endocytosis / response to cold / G protein-coupled receptor activity / viral release from host cell by cytolysis / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / ADORA2B mediated anti-inflammatory cytokines production / positive regulation of protein serine/threonine kinase activity / peptidoglycan catabolic process / clathrin-coated endocytic vesicle membrane / G alpha (s) signalling events / cellular response to amyloid-beta / positive regulation of cold-induced thermogenesis / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / cell wall macromolecule catabolic process / amyloid-beta binding / lysozyme / lysozyme activity / cytolysis / positive regulation of MAPK cascade / lysosome / apical plasma membrane / cell surface receptor signaling pathway / endosome membrane / early endosome / Ub-specific processing proteases / receptor complex / endosome / host cell cytoplasm / defense response to bacterium / protein-containing complex binding / Golgi apparatus / integral component of plasma membrane / positive regulation of transcription by RNA polymerase II / protein homodimerization activity / membrane / identical protein binding / plasma membrane / nucleus
Similarity search - Function
Beta 2 adrenoceptor / Adrenoceptor family / Rhodopsin 7-helix transmembrane proteins / Rhopdopsin 7-helix transmembrane proteins / Serpentine type 7TM GPCR chemoreceptor Srsx / Lysozyme - #40 / Endolysin T4 type / T4-type lysozyme / Lysozyme domain superfamily / Glycoside hydrolase, family 24 ...Beta 2 adrenoceptor / Adrenoceptor family / Rhodopsin 7-helix transmembrane proteins / Rhopdopsin 7-helix transmembrane proteins / Serpentine type 7TM GPCR chemoreceptor Srsx / Lysozyme - #40 / Endolysin T4 type / T4-type lysozyme / Lysozyme domain superfamily / Glycoside hydrolase, family 24 / Phage lysozyme / G-protein coupled receptors family 1 signature. / 7 transmembrane receptor (rhodopsin family) / G-protein coupled receptors family 1 profile. / GPCR, rhodopsin-like, 7TM / G protein-coupled receptor, rhodopsin-like / Lysozyme / Lysozyme-like domain superfamily / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Endolysin / CHOLESTEROL / Chem-JSZ / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Beta-2 adrenergic receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Enterobacteria phage T4 (bacteriophage)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.84 Å
AuthorsFenalti, G. / Wacker, D. / Brown, M.A. / Katritch, V. / Abagyan, R. / Cherezov, V. / Stevens, R.C. / Accelerated Technologies Center for Gene to 3D Structure (ATCG3D) / GPCR Network (GPCR)
CitationJournal: J.Am.Chem.Soc. / Year: 2010
Title: Conserved Binding Mode of Human beta(2) Adrenergic Receptor Inverse Agonists and Antagonist Revealed by X-ray Crystallography
Authors: Wacker, D. / Fenalti, G. / Brown, M.A. / Katritch, V. / Abagyan, R. / Cherezov, V. / Stevens, R.C.
History
DepositionJul 14, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 23, 2012Group: Database references
Revision 1.3Aug 8, 2012Group: Other
Revision 1.4Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Beta-2 adrenergic receptor, Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4235
Polymers55,9581
Non-polymers1,4654
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.580, 75.900, 174.180
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Beta-2 adrenergic receptor, Lysozyme / / Beta-2 adrenoreceptor / Beta-2 adrenoceptor / Lysis protein / Muramidase / Endolysin


Mass: 55957.926 Da / Num. of mol.: 1
Fragment: Chimeric protein of Beta-2 Adrenoreceptor 1-230, Lysozyme 2-161, Beta-2 adrenergic receptor 263-348
Mutation: E122W, N187E, C1054T, C1097A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Enterobacteria phage T4 (bacteriophage)
Gene: ADRB2, ADRB2R, B2AR, E / Plasmid: PFASTBAC / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: P07550, UniProt: P00720
#2: Chemical ChemComp-CLR / CHOLESTEROL / Cholesterol


Mass: 386.654 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H46O
#3: Chemical ChemComp-JSZ / ethyl 4-({(2S)-2-hydroxy-3-[(1-methylethyl)amino]propyl}oxy)-3-methyl-1-benzofuran-2-carboxylate


Mass: 335.395 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H25NO5
#4: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H40O4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 10

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.68 %
Crystal growTemperature: 293 K
Details: 100 mM Tris/HCl pH 7.5-8, 5% 1,4 butanediol, 220 mM Na-formate, 27% PEG 400, Lipidic Cubic Phase (LCP) Crystallization, temperature 293-295K
PH range: 7.5-8.0

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 23-ID-D11.0332
SYNCHROTRONAPS 23-ID-D21.0332
Detector
TypeIDDetectorDate
MARMOSAIC 300 mm CCD1CCDNov 19, 2009
MARMOSAIC 300 mm CCD2CCDDec 10, 2009
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double CrystalSINGLE WAVELENGTHMx-ray1
2Double CrystalSINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.84→40 Å / Num. all: 13388 / Num. obs: 12234 / % possible obs: 91.4 % / Observed criterion σ(I): -3 / Redundancy: 3.84 % / Rsym value: 0.131 / Net I/σ(I): 7.08
Reflection shellResolution: 2.84→2.98 Å / Redundancy: 2.93 % / Mean I/σ(I) obs: 1.99 / Num. unique all: 1749 / Rsym value: 0.43 / % possible all: 82

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.5.0102refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3D4S
Resolution: 2.84→37.77 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.889 / SU B: 19.156 / SU ML: 0.372 / Cross valid method: THROUGHOUT / ESU R Free: 0.446 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27839 612 5 %RANDOM
Rwork0.21889 ---
obs0.22183 11620 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 58.384 Å2
Baniso -1Baniso -2Baniso -3
1-5.7 Å20 Å20 Å2
2---0.74 Å20 Å2
3----4.96 Å2
Refinement stepCycle: LAST / Resolution: 2.84→37.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3466 0 105 8 3579
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223660
X-RAY DIFFRACTIONr_angle_refined_deg1.231.9714986
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8785438
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.84323.082146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.67715585
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6531520
X-RAY DIFFRACTIONr_chiral_restr0.0830.2589
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022647
LS refinement shellResolution: 2.84→2.913 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 38 -
Rwork0.312 730 -
obs--100 %

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