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- PDB-3p0g: Structure of a nanobody-stabilized active state of the beta2 adre... -

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Basic information

Entry
Database: PDB / ID: 3p0g
TitleStructure of a nanobody-stabilized active state of the beta2 adrenoceptor
Components
  • Beta-2 adrenergic receptor, Lysozyme
  • Camelid Antibody Fragment
KeywordsSIGNALING PROTEIN / Hydrolase / BETA-2 ADRENOCEPTOR / agonist / nanobody / 7TM / GPCR / membrane / membrane protein
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 / adenylate cyclase binding / smooth muscle contraction / potassium channel regulator activity / positive regulation of bone mineralization / 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 / response to cold / peptidoglycan catabolic process / 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 / amyloid-beta binding / positive regulation of cold-induced thermogenesis / G alpha (s) signalling events / host cell cytoplasm / positive regulation of MAPK cascade / transcription by RNA polymerase II / lysosome / cell surface receptor signaling pathway / 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 / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / Serpentine type 7TM GPCR chemoreceptor Srsx ...Beta 2 adrenoceptor / Adrenoceptor family / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / 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 / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Chem-P0G / Endolysin / Beta-2 adrenergic receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Enterobacteria phage T4 (virus)
LAMA GLAMA (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsRasmussen, S.G.F. / Choi, H.-J. / Fung, J.J. / Pardon, E. / Casarosa, P. / Chae, P.S. / DeVree, B.T. / Rosenbaum, D.M. / Thian, F.S. / Kobilka, T.S. ...Rasmussen, S.G.F. / Choi, H.-J. / Fung, J.J. / Pardon, E. / Casarosa, P. / Chae, P.S. / DeVree, B.T. / Rosenbaum, D.M. / Thian, F.S. / Kobilka, T.S. / Schnapp, A. / Konetzki, I. / Sunahara, R.K. / Gellman, S.H. / Pautsch, A. / Steyaert, J. / Weis, W.I. / Kobilka, B.K.
CitationJournal: Nature / Year: 2011
Title: Structure of a nanobody-stabilized active state of the b2 adrenoceptor
Authors: Rasmussen, S.G. / Choi, H.J. / Fung, J.J. / Pardon, E. / Casarosa, P. / Chae, P.S. / Devree, B.T. / Rosenbaum, D.M. / Thian, F.S. / Kobilka, T.S. / Schnapp, A. / Konetzki, I. / Sunahara, R.K. ...Authors: Rasmussen, S.G. / Choi, H.J. / Fung, J.J. / Pardon, E. / Casarosa, P. / Chae, P.S. / Devree, B.T. / Rosenbaum, D.M. / Thian, F.S. / Kobilka, T.S. / Schnapp, A. / Konetzki, I. / Sunahara, R.K. / Gellman, S.H. / Pautsch, A. / Steyaert, J. / Weis, W.I. / Kobilka, B.K.
History
DepositionSep 28, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 23, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-2 adrenergic receptor, Lysozyme
B: Camelid Antibody Fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,8713
Polymers70,5012
Non-polymers3701
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-19 kcal/mol
Surface area20570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)236.686, 45.660, 71.375
Angle α, β, γ (deg.)90.00, 102.34, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 56716.531 Da / Num. of mol.: 1
Fragment: UNP P07550 residues 1-230, 263-365, UNP P00720 residues 2-161
Mutation: N187E
Source method: isolated from a genetically manipulated source
Details: BETA-2-ADRENERGIC RECEPTOR/T4-LYSOZYME CHIMERA
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Enterobacteria phage T4 (virus)
Gene: ADRB2, ADRB2R, B2AR, E / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P07550, UniProt: P00720, lysozyme
#2: Antibody Camelid Antibody Fragment


Mass: 13784.176 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: NANOBODY / Source: (gene. exp.) LAMA GLAMA (llama) / Production host: Escherichia coli (E. coli)
#3: 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.: 1 / Source method: obtained synthetically / Formula: C21H26N2O4
Compound detailsTHE T4 LYSOZYME IS NOT VISIBLE IN THE STRUCTURE
Sequence detailsSEQUENCE CONFLICT AT THESE POSITION IN UNP ENTRY P07550

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 23

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Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.97 %
Crystal growTemperature: 293 K / pH: 8
Details: 36-44% PEG 400, 100 mM Tris pH 8.0, 4% DMSO, 1% 1,2,3-heptanetriol, twin-syringe mixing method, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1781
2781
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 23-ID-B11.0332
SYNCHROTRONAPS 23-ID-B21.0332
Detector
TypeIDDetectorDateDetails
MARMOSAIC 300 mm CCD1CCDMar 10, 2010mirrors
MARMOSAIC 300 mm CCD2CCDMar 25, 2010mirrors
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: 3.5→50 Å / Num. obs: 9308 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 45.69 Å2 / Rmerge(I) obs: 0.2 / Net I/σ(I): 4.9
Reflection shellResolution: 3.5→3.56 Å / % possible all: 93.7

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Processing

Software
NameVersionClassificationNB
BUSTER-TNTBUSTER 2.8.0refinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
BUSTER2.8.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 2RH1 and 3DWT

2rh1

3dwt


Resolution: 3.5→37 Å / Cor.coef. Fo:Fc: 0.8383 / Cor.coef. Fo:Fc free: 0.7237 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.3083 937 10.17 %RANDOM
Rwork0.2354 ---
obs0.2428 9210 --
Displacement parametersBiso mean: 79.94 Å2
Baniso -1Baniso -2Baniso -3
1-33.1715 Å20 Å24.3275 Å2
2--2.9707 Å20 Å2
3----36.1422 Å2
Refine analyzeLuzzati coordinate error obs: 0.746 Å
Refinement stepCycle: LAST / Resolution: 3.5→37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3211 0 27 0 3238
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013321HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.224521HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1095SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes64HARMONIC2
X-RAY DIFFRACTIONt_gen_planes482HARMONIC5
X-RAY DIFFRACTIONt_it3292HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.57
X-RAY DIFFRACTIONt_other_torsion25.21
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion4475
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact39454
LS refinement shellResolution: 3.5→3.91 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.3103 262 10.16 %
Rwork0.2344 2316 -
all0.2422 2578 -

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