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- PDB-6oba: The beta2 adrenergic receptor bound to a negative allosteric modulator -

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Basic information

Entry
Database: PDB / ID: 6oba
TitleThe beta2 adrenergic receptor bound to a negative allosteric modulator
ComponentsBeta-2 adrenergic receptor,Lysozyme,Beta-2 adrenergic receptor
KeywordsSIGNALING PROTEIN / G protein coupled receptors / signal transduction / allosteric modulators / membrane protein
Function / homology
Function and homology information


: / beta2-adrenergic receptor activity / 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 / norepinephrine-epinephrine-mediated vasodilation involved in regulation of systemic arterial blood pressure ...: / beta2-adrenergic receptor activity / 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 / norepinephrine-epinephrine-mediated vasodilation involved in regulation of systemic arterial blood pressure / 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 / adrenergic receptor signaling pathway / endosome to lysosome transport / diet induced thermogenesis / neuronal dense core vesicle / positive regulation of protein kinase A signaling / adenylate cyclase binding / smooth muscle contraction / potassium channel regulator activity / positive regulation of bone mineralization / brown fat cell differentiation / adenylate cyclase-activating adrenergic receptor signaling pathway / regulation of sodium ion transport / bone resorption / viral release from host cell by cytolysis / activation of adenylate cyclase activity / response to cold / peptidoglycan catabolic process / receptor-mediated endocytosis / clathrin-coated endocytic vesicle membrane / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / positive regulation of protein serine/threonine kinase activity / cellular response to amyloid-beta / cell wall macromolecule catabolic process / Cargo recognition for clathrin-mediated endocytosis / lysozyme / Clathrin-mediated endocytosis / lysozyme activity / positive regulation of cold-induced thermogenesis / amyloid-beta binding / G alpha (s) signalling events / host cell cytoplasm / transcription by RNA polymerase II / positive regulation of MAPK cascade / cell surface receptor signaling pathway / lysosome / early endosome / receptor complex / endosome membrane / Ub-specific processing proteases / endosome / defense response to bacterium / apical plasma membrane / protein-containing complex binding / Golgi apparatus / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / membrane / identical protein binding / nucleus / plasma membrane
Similarity search - Function
Beta 2 adrenoceptor / Adrenoceptor family / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like ...Beta 2 adrenoceptor / Adrenoceptor family / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / 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) / Lysozyme-like domain superfamily
Similarity search - Domain/homology
CHOLESTEROL / Chem-JTZ / 6-bromo-N~2~-phenylquinazoline-2,4-diamine / Endolysin / Beta-2 adrenergic receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Enterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsLiu, X. / Stobel, A. / Kaindl, J. / Dengler, D. / ClarK, M. / Mahoney, J. / Korczynska, M. / Matt, R.A. / Hubner, H. / Xu, X. ...Liu, X. / Stobel, A. / Kaindl, J. / Dengler, D. / ClarK, M. / Mahoney, J. / Korczynska, M. / Matt, R.A. / Hubner, H. / Xu, X. / Stanek, M. / Hirata, K. / Shoichet, B. / Sunahara, R. / Gmeiner, R. / Kobilka, B.K.
CitationJournal: Nat.Chem.Biol. / Year: 2020
Title: An allosteric modulator binds to a conformational hub in the beta2adrenergic receptor.
Authors: Liu, X. / Kaindl, J. / Korczynska, M. / Stossel, A. / Dengler, D. / Stanek, M. / Hubner, H. / Clark, M.J. / Mahoney, J. / Matt, R.A. / Xu, X. / Hirata, K. / Shoichet, B.K. / Sunahara, R.K. / ...Authors: Liu, X. / Kaindl, J. / Korczynska, M. / Stossel, A. / Dengler, D. / Stanek, M. / Hubner, H. / Clark, M.J. / Mahoney, J. / Matt, R.A. / Xu, X. / Hirata, K. / Shoichet, B.K. / Sunahara, R.K. / Kobilka, B.K. / Gmeiner, P.
History
DepositionMar 20, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jul 8, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)57,9395
Polymers56,6011
Non-polymers1,3384
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-1 kcal/mol
Surface area21830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.460, 75.710, 173.410
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 adrenergic receptor / Beta-2 adrenoreceptor / Beta-2 adrenoceptor


Mass: 56601.438 Da / Num. of mol.: 1
Fragment: beta-2 (UNP residues 1-230), lysozyme, beta-2 (UNP residues 264-365)
Mutation: N187E, C1054T, C1097A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Enterobacteria phage T4 (virus)
Gene: ADRB2, ADRB2R, B2AR, e, T4Tp126 / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P07550, UniProt: D9IEF7, lysozyme
#2: Chemical ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H46O
#3: Chemical ChemComp-JTZ / (2S)-1-[(1-methylethyl)amino]-3-(2-prop-2-en-1-ylphenoxy)propan-2-ol


Mass: 249.349 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23NO2
#4: Chemical ChemComp-M3J / 6-bromo-N~2~-phenylquinazoline-2,4-diamine


Mass: 315.168 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H11BrN4 / Feature type: SUBJECT OF INVESTIGATION

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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: 2.35 Å3/Da / Density % sol: 47.57 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 8
Details: 0.1 M Tris-HCl, pH 8.0, 30-40% PEG400, 300-400 mM sodium formate, 6% 1,4-butanediol, 1 mM alprenolol, 1 mM AS408, 1% DMSO

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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: Dec 9, 2016
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→45.9 Å / Num. obs: 10168 / % possible obs: 99.1 % / Redundancy: 13.3 % / CC1/2: 0.996 / Net I/σ(I): 8.5
Reflection shellResolution: 3.1→3.2 Å / Redundancy: 9.7 % / Mean I/σ(I) obs: 1.27 / Num. unique obs: 886 / CC1/2: 0.685 / % possible all: 98.2

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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 2RH1

2rh1


Resolution: 3.1→19.977 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 30.04
RfactorNum. reflection% reflection
Rfree0.2772 994 9.83 %
Rwork0.251 --
obs0.2536 10109 99.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.1→19.977 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3523 0 93 0 3616
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083707
X-RAY DIFFRACTIONf_angle_d0.7495045
X-RAY DIFFRACTIONf_dihedral_angle_d13.6351308
X-RAY DIFFRACTIONf_chiral_restr0.44586
X-RAY DIFFRACTIONf_plane_restr0.003604
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.26280.38251350.37571256X-RAY DIFFRACTION98
3.2628-3.46620.33311400.32141263X-RAY DIFFRACTION99
3.4662-3.73230.3361430.30041287X-RAY DIFFRACTION99
3.7323-4.10490.2951380.27641291X-RAY DIFFRACTION100
4.1049-4.69220.27261410.23211296X-RAY DIFFRACTION100
4.6922-5.88650.28071440.26211322X-RAY DIFFRACTION99
5.8865-19.9770.22131530.18981400X-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)
13.29790.2164-1.14014.2194-0.33755.2577-0.1043-0.0959-0.03150.29430.15760.08580.1858-0.1671-0.05750.6801-0.04070.00660.42240.02440.43661.83416.596540.4775
22.91440.0085-1.14744.7233-0.25824.50350.15320.01660.074-0.0812-0.02810.0038-0.56080.2184-0.11650.724-0.03310.11130.78090.11150.56519.1107-1.0957-0.4948
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1resseq 31-342 or resseq 1201-1204
2X-RAY DIFFRACTION2resseq 1002:1161

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