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- PDB-6kr8: Structure of the beta2 adrenergic receptor in the full agonist bo... -

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Basic information

Entry
Database: PDB / ID: 6kr8
TitleStructure of the beta2 adrenergic receptor in the full agonist bound state
Componentsbeta 2 adrenergic receptor
KeywordsMEMBRANE PROTEIN / G-protein coupled receptor / b2AR / full agonist
Function / homology
Function and homology information


positive regulation of mini excitatory postsynaptic potential / beta2-adrenergic receptor activity / negative regulation of smooth muscle contraction / AMPA selective glutamate receptor signaling pathway / positive regulation of autophagosome maturation / norepinephrine-epinephrine-mediated vasodilation involved in regulation of systemic arterial blood pressure / heat generation / norepinephrine binding / Adrenoceptors / positive regulation of lipophagy ...positive regulation of mini excitatory postsynaptic potential / beta2-adrenergic receptor activity / negative regulation of smooth muscle contraction / AMPA selective glutamate receptor signaling pathway / positive regulation of autophagosome maturation / norepinephrine-epinephrine-mediated vasodilation involved in regulation of systemic arterial blood pressure / heat generation / norepinephrine binding / Adrenoceptors / positive regulation of lipophagy / negative regulation of multicellular organism growth / negative regulation of G protein-coupled receptor signaling pathway / endosome to lysosome transport / response to psychosocial stress / adrenergic receptor signaling pathway / diet induced thermogenesis / positive regulation of cAMP/PKA signal transduction / adenylate cyclase binding / smooth muscle contraction / bone resorption / positive regulation of bone mineralization / potassium channel regulator activity / neuronal dense core vesicle / brown fat cell differentiation / intercellular bridge / regulation of sodium ion transport / adenylate cyclase-activating adrenergic receptor signaling pathway / receptor-mediated endocytosis / response to cold / clathrin-coated endocytic vesicle membrane / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / cellular response to amyloid-beta / mitotic spindle / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / positive regulation of cold-induced thermogenesis / amyloid-beta binding / microtubule cytoskeleton / G alpha (s) signalling events / transcription by RNA polymerase II / early endosome / cell surface receptor signaling pathway / lysosome / receptor complex / positive regulation of MAPK cascade / endosome / endosome membrane / Ub-specific processing proteases / cilium / ciliary basal body / apical plasma membrane / protein-containing complex binding / Golgi apparatus / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / identical protein binding / nucleus / membrane / plasma membrane
Similarity search - Function
Beta 2 adrenoceptor / Adrenoceptor family / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / 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) ...Beta 2 adrenoceptor / Adrenoceptor family / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / 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
Beta-2 adrenergic receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsImai, S. / Shimada, I.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED) Japan
Japan Society for the Promotion of Science Japan
CitationJournal: Nat.Chem.Biol. / Year: 2020
Title: Structural equilibrium underlying ligand-dependent activation of beta2-adrenoreceptor.
Authors: Imai, S. / Yokomizo, T. / Kofuku, Y. / Shiraishi, Y. / Ueda, T. / Shimada, I.
History
DepositionAug 21, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2020Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Apr 8, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: beta 2 adrenergic receptor


Theoretical massNumber of molelcules
Total (without water)38,5581
Polymers38,5581
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area19400 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 500structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein beta 2 adrenergic receptor


Mass: 38557.980 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P07550*PLUS
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
122isotropic12D 1H-15N HSQC
133isotropic12D 1H-15N HSQC
144isotropic12D 1H-15N HSQC
155isotropic12D 1H-15N HSQC
166isotropic12D 1H-15N HSQC
177isotropic12D 1H-15N HSQC
188isotropic12D 1H-15N HSQC
199isotropic12D 1H-15N HSQC
11010isotropic12D 1H-15N HSQC
11111isotropic12D 1H-15N HSQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
micelle120 mM HEPES, 100 uM [2,3,3-2H,15N]-Leu beta 2 adrenergic receptor (A59C-MTSL), 95% H2O/5% D2OA59C-MTSL (paramagnetic)95% H2O/5% D2O
micelle220 mM HEPES, 100 uM [2,3,3-2H,15N]-Leu beta 2 adrenergic receptor (A59C-MTSL), 1 mM ascorbate, 95% H2O/5% D2OA59C-MTSL (diamagnetic)95% H2O/5% D2O
micelle320 mM HEPES, 100 uM [2,3,3-2H,15N]-Leu beta 2 adrenergic receptor (T136C-MTSL), 95% H2O/5% D2OT136C-MTSL (paramagnetic)95% H2O/5% D2O
micelle420 mM HEPES, 100 uM [2,3,3-2H,15N]-Leu beta 2 adrenergic receptor (T136C-MTSL), 1 mM ascorbate, 95% H2O/5% D2OT136C-MTSL (diamagnetic)95% H2O/5% D2O
micelle520 mM HEPES, 100 uM [2,3,3-2H,15N]-Leu beta 2 adrenergic receptor (N148C-MTSL), 95% H2O/5% D2ON148C-MTSL (paramagnetic)95% H2O/5% D2O
micelle620 mM HEPES, 100 uM [2,3,3-2H,15N]-Leu beta 2 adrenergic receptor (N148C-MTSL), 1 mM ascorbate, 95% H2O/5% D2ON148C-MTSL (diamagnetic)95% H2O/5% D2O
micelle720 mM HEPES, 100 uM [2,3,3-2H,15N]-Leu beta 2 adrenergic receptor (L266C-MTSL), 95% H2O/5% D2OL266C-MTSL (paramagnetic)95% H2O/5% D2O
micelle820 mM HEPES, 100 uM [2,3,3-2H,15N]-Leu beta 2 adrenergic receptor (L266C-MTSL), 1 mM ascorbate, 95% H2O/5% D2OL266C-MTSL (diamagnetic)95% H2O/5% D2O
micelle920 mM HEPES, 100 uM [2,3,3-2H,15N]-Leu beta 2 adrenergic receptor (I334C-MTSL), 95% H2O/5% D2OI334C-MTSL (paramagnetic)95% H2O/5% D2O
micelle1020 mM HEPES, 100 uM [2,3,3-2H,15N]-Leu beta 2 adrenergic receptor (I334C-MTSL), 1 mM ascorbate, 95% H2O/5% D2OI334C-MTSL (diamagnetic)95% H2O/5% D2O
micelle1120 mM HEPES, 100 uM [2,3,3-2H,15N]-Leu beta 2 adrenergic receptor (I334C-MTSL), 95% H2O/5% D2Ob2AR-D95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMHEPESnatural abundance1
100 uMbeta 2 adrenergic receptor (A59C-MTSL)[2,3,3-2H,15N]-Leu1
20 mMHEPESnatural abundance2
100 uMbeta 2 adrenergic receptor (A59C-MTSL)[2,3,3-2H,15N]-Leu2
1 mMascorbatenatural abundance2
20 mMHEPESnatural abundance3
100 uMbeta 2 adrenergic receptor (T136C-MTSL)[2,3,3-2H,15N]-Leu3
20 mMHEPESnatural abundance4
100 uMbeta 2 adrenergic receptor (T136C-MTSL)[2,3,3-2H,15N]-Leu4
1 mMascorbatenatural abundance4
20 mMHEPESnatural abundance5
100 uMbeta 2 adrenergic receptor (N148C-MTSL)[2,3,3-2H,15N]-Leu5
20 mMHEPESnatural abundance6
100 uMbeta 2 adrenergic receptor (N148C-MTSL)[2,3,3-2H,15N]-Leu6
1 mMascorbatenatural abundance6
20 mMHEPESnatural abundance7
100 uMbeta 2 adrenergic receptor (L266C-MTSL)[2,3,3-2H,15N]-Leu7
20 mMHEPESnatural abundance8
100 uMbeta 2 adrenergic receptor (L266C-MTSL)[2,3,3-2H,15N]-Leu8
1 mMascorbatenatural abundance8
20 mMHEPESnatural abundance9
100 uMbeta 2 adrenergic receptor (I334C-MTSL)[2,3,3-2H,15N]-Leu9
20 mMHEPESnatural abundance10
100 uMbeta 2 adrenergic receptor (I334C-MTSL)[2,3,3-2H,15N]-Leu10
1 mMascorbatenatural abundance10
20 mMHEPESnatural abundance11
100 uMbeta 2 adrenergic receptor (I334C-MTSL)[2,3,3-2H,15N]-Leu11
Sample conditionsIonic strength: 0 mM / Label: condition_1 / pH: 6.5 / PH err: 0.1 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
CNSBrunger A. T. et.al.refinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
TopSpinBruker Biospinchemical shift assignment
TopSpinBruker Biospinpeak picking
RefinementMethod: simulated annealing / Software ordinal: 2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 500 / Conformers submitted total number: 10

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