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- PDB-6e67: Structure of beta2 adrenergic receptor fused to a Gs peptide -

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Basic information

Entry
Database: PDB / ID: 6.0E+67
TitleStructure of beta2 adrenergic receptor fused to a Gs peptide
ComponentsBeta-2 adrenergic receptor,Endolysin,Guanine nucleotide-binding protein G(s) subunit alpha isoforms short,Beta-2 adrenergic receptor chimera
KeywordsMEMBRANE PROTEIN / G protein coupled Receptor
Function / homology
Function and homology information


desensitization of G protein-coupled receptor signaling pathway by arrestin / beta2-adrenergic receptor activity / norepinephrine-epinephrine-mediated vasodilation involved in regulation of systemic arterial blood pressure / positive regulation of mini excitatory postsynaptic potential / positive regulation of cAMP-dependent protein kinase activity / norepinephrine binding / Adrenoceptors / heat generation / positive regulation of autophagosome maturation / positive regulation of AMPA receptor activity ...desensitization of G protein-coupled receptor signaling pathway by arrestin / beta2-adrenergic receptor activity / norepinephrine-epinephrine-mediated vasodilation involved in regulation of systemic arterial blood pressure / positive regulation of mini excitatory postsynaptic potential / positive regulation of cAMP-dependent protein kinase activity / norepinephrine binding / Adrenoceptors / heat generation / positive regulation of autophagosome maturation / positive regulation of AMPA receptor activity / activation of transmembrane receptor protein tyrosine kinase activity / negative regulation of smooth muscle contraction / positive regulation of lipophagy / response to psychosocial stress / negative regulation of multicellular organism growth / endosome to lysosome transport / adrenergic receptor signaling pathway / diet induced thermogenesis / neuronal dense core vesicle / positive regulation of protein kinase A signaling / PKA activation in glucagon signalling / hair follicle placode formation / adenylate cyclase binding / intracellular transport / D1 dopamine receptor binding / smooth muscle contraction / developmental growth / potassium channel regulator activity / Hedgehog 'off' state / positive regulation of bone mineralization / positive regulation of cAMP-mediated signaling / adenylate cyclase-activating adrenergic receptor signaling pathway / brown fat cell differentiation / regulation of sodium ion transport / bone resorption / viral release from host cell by cytolysis / activation of adenylate cyclase activity / receptor-mediated endocytosis / adenylate cyclase activator activity / response to cold / peptidoglycan catabolic process / trans-Golgi network membrane / clathrin-coated endocytic vesicle membrane / G-protein beta/gamma-subunit complex binding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / bone development / positive regulation of protein serine/threonine kinase activity / Prostacyclin signalling through prostacyclin receptor / Glucagon signaling in metabolic regulation / adenylate cyclase-activating G protein-coupled receptor signaling pathway / platelet aggregation / Glucagon-type ligand receptors / cognition / Vasopressin regulates renal water homeostasis via Aquaporins / positive regulation of GTPase activity / G alpha (z) signalling events / cellular response to catecholamine stimulus / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADORA2B mediated anti-inflammatory cytokines production / adenylate cyclase-activating dopamine receptor signaling pathway / cellular response to prostaglandin E stimulus / GPER1 signaling / cellular response to amyloid-beta / heterotrimeric G-protein complex / sensory perception of smell / cell wall macromolecule catabolic process / Cargo recognition for clathrin-mediated endocytosis / lysozyme / Clathrin-mediated endocytosis / lysozyme activity / amyloid-beta binding / positive regulation of cold-induced thermogenesis / G alpha (i) signalling events / G alpha (s) signalling events / host cell cytoplasm / positive regulation of MAPK cascade / transcription by RNA polymerase II / lysosome / cell surface receptor signaling pathway / receptor complex / early endosome / endosome membrane / Ub-specific processing proteases / endosome / defense response to bacterium / apical plasma membrane / GTPase activity / protein-containing complex binding / GTP binding / Golgi apparatus / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular exosome / membrane / identical protein binding / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Beta 2 adrenoceptor / Adrenoceptor family / G-protein alpha subunit, group S / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / Serpentine type 7TM GPCR chemoreceptor Srsx / G-alpha domain profile. ...Beta 2 adrenoceptor / Adrenoceptor family / G-protein alpha subunit, group S / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / Serpentine type 7TM GPCR chemoreceptor Srsx / G-alpha domain profile. / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G protein alpha subunit / 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) / Lysozyme-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Chem-P0G / Endolysin / Beta-2 adrenergic receptor / Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
Similarity search - Component
Biological speciesHomo sapiens (human)
Enterobacteria phage RB59 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.7 Å
AuthorsLiu, X. / Xu, X. / Hilger, D. / Tiemann, J. / Liu, H. / Du, Y. / Hirata, K. / Sun, X. / Guixa-Gonzalez, R. / Mathiesen, J. ...Liu, X. / Xu, X. / Hilger, D. / Tiemann, J. / Liu, H. / Du, Y. / Hirata, K. / Sun, X. / Guixa-Gonzalez, R. / Mathiesen, J. / Hildebrand, P. / Kobilka, B.
CitationJournal: Cell / Year: 2019
Title: Structural Insights into the Process of GPCR-G Protein Complex Formation.
Authors: Liu, X. / Xu, X. / Hilger, D. / Aschauer, P. / Tiemann, J.K.S. / Du, Y. / Liu, H. / Hirata, K. / Sun, X. / Guixa-Gonzalez, R. / Mathiesen, J.M. / Hildebrand, P.W. / Kobilka, B.K.
History
DepositionJul 24, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-2 adrenergic receptor,Endolysin,Guanine nucleotide-binding protein G(s) subunit alpha isoforms short,Beta-2 adrenergic receptor chimera
B: Beta-2 adrenergic receptor,Endolysin,Guanine nucleotide-binding protein G(s) subunit alpha isoforms short,Beta-2 adrenergic receptor chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,0584
Polymers120,3172
Non-polymers7412
Water0
1
A: Beta-2 adrenergic receptor,Endolysin,Guanine nucleotide-binding protein G(s) subunit alpha isoforms short,Beta-2 adrenergic receptor chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,5292
Polymers60,1591
Non-polymers3701
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-2 adrenergic receptor,Endolysin,Guanine nucleotide-binding protein G(s) subunit alpha isoforms short,Beta-2 adrenergic receptor chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,5292
Polymers60,1591
Non-polymers3701
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.010, 377.440, 45.590
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Beta-2 adrenergic receptor,Endolysin,Guanine nucleotide-binding protein G(s) subunit alpha isoforms short,Beta-2 adrenergic receptor chimera / Beta-2 adrenoreceptor / Beta-2 adrenoceptor / Lysis protein / Lysozyme / Muramidase / Adenylate ...Beta-2 adrenoreceptor / Beta-2 adrenoceptor / Lysis protein / Lysozyme / Muramidase / Adenylate cyclase-stimulating G alpha protein / Beta-2 adrenoreceptor / Beta-2 adrenoceptor


Mass: 60158.539 Da / Num. of mol.: 2
Fragment: beta-2 (UNP residues 1-232), lysozyme (UNP residues 2-161), GS (UNP residues 1024-1036)
Mutation: M96T, M98T, N187E, C22A, C1054T, C1097A,M96T, M98T, N187E, C1054T, C1097A,M96T, M98T, N187E, C1054T, C1097A,M96T, M98T, N187E, C1054T, C1097A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Enterobacteria phage RB59 (virus)
Gene: ADRB2, ADRB2R, B2AR, e, RB59_126, GNAS, GNAS1, GSP / Plasmid: pvl1392 / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P07550, UniProt: A0A097J809, UniProt: P63092, lysozyme
#2: Chemical ChemComp-P0G / 8-[(1R)-2-{[1,1-dimethyl-2-(2-methylphenyl)ethyl]amino}-1-hydroxyethyl]-5-hydroxy-2H-1,4-benzoxazin-3(4H)-one


Mass: 370.442 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H26N2O4

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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: 3.11 Å3/Da / Density % sol: 60.9 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 7
Details: 100 mM Bis-Tris, pH 7.0, 75-125 mM ammonium acetate, 50-75 mM potassium fluoride, 38-42% PEG400, 6% ethylene glycol, 1.5% 1,2-propaneiol

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 11, 2016
RadiationMonochromator: liquid nitrogen-cooled double crystal Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.7→45.6 Å / Num. obs: 16163 / % possible obs: 99 % / Redundancy: 7.5 % / CC1/2: 0.98 / Net I/σ(I): 4.15
Reflection shellResolution: 3.7→3.8 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 1.05 / Num. unique obs: 1257 / CC1/2: 0.51 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4LDE

4lde


Resolution: 3.7→19.98 Å / SU ML: 0.56 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3072 1598 10 %
Rwork0.2764 --
obs0.2794 15987 99.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.7→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7153 0 54 0 7207
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037379
X-RAY DIFFRACTIONf_angle_d0.43310092
X-RAY DIFFRACTIONf_dihedral_angle_d9.974274
X-RAY DIFFRACTIONf_chiral_restr0.0361192
X-RAY DIFFRACTIONf_plane_restr0.0041256
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.7-3.81870.39551440.36921296X-RAY DIFFRACTION98
3.8187-3.95410.41271400.34241254X-RAY DIFFRACTION99
3.9541-4.11110.34761460.33051313X-RAY DIFFRACTION100
4.1111-4.29650.34851390.29691260X-RAY DIFFRACTION100
4.2965-4.52050.32721460.28871308X-RAY DIFFRACTION100
4.5205-4.80010.30631400.28141265X-RAY DIFFRACTION99
4.8001-5.16480.30591480.28551327X-RAY DIFFRACTION99
5.1648-5.67370.27881440.30271306X-RAY DIFFRACTION99
5.6737-6.47020.37541480.31851319X-RAY DIFFRACTION99
6.4702-8.06170.28491460.26561322X-RAY DIFFRACTION99
8.0617-19.98030.23121570.19231419X-RAY DIFFRACTION99
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)
12.80680.0869-0.76720.8190.10282.1559-0.12310.1387-0.3936-0.30680.0965-0.14560.24190.02950.02740.6178-0.03890.07870.66-0.00970.7246-67.3041432.241821.7794
22.90230.57860.04071.58860.41782.0095-0.06630.4420.6092-0.2090.09210.383-0.3327-0.20580.12031.21090.0029-0.00591.06460.0620.9973-81.164472.731112.6035
32.912-0.6533-1.33783.54171.69222.49690.2268-0.0490.23350.0554-0.2372-0.0528-0.18140.06170.07040.6796-0.00020.04760.7389-0.03020.6084-27.4313427.966410.3775
41.4406-0.1731-0.63872.4547-1.22393.00060.3763-0.1573-0.19050.1819-0.25910.5342-0.2176-0.0789-0.11890.76720.00550.04910.6568-0.0271.0537-9.0124390.2231-1.7989
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resseq 29:343 or chain A and resseq 3101
2X-RAY DIFFRACTION2chain A and resseq 1002:3003
3X-RAY DIFFRACTION3chain B and resseq 29:343 or chain B and resseq 3101
4X-RAY DIFFRACTION4chain B and resseq 1002:3003

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