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- PDB-3pds: Irreversible Agonist-Beta2 Adrenoceptor Complex -

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Basic information

Entry
Database: PDB / ID: 3pds
TitleIrreversible Agonist-Beta2 Adrenoceptor Complex
ComponentsFusion protein Beta-2 adrenergic receptor/Lysozyme
KeywordsMembrane Protein/Hydrolase / GPCR / signaling / beta adrenergic agonist / fusion protein / Membrane Protein-Hydrolase complex
Function / homology
Function and homology information


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 / positive regulation of AMPA receptor activity / norepinephrine binding / positive regulation of autophagosome maturation / heat generation / Adrenoceptors / activation of transmembrane receptor protein tyrosine kinase activity ...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 / positive regulation of AMPA receptor activity / norepinephrine binding / positive regulation of autophagosome maturation / heat generation / Adrenoceptors / activation of transmembrane receptor protein tyrosine kinase activity / negative regulation of smooth muscle contraction / positive regulation of lipophagy / negative regulation of multicellular organism growth / negative regulation of G protein-coupled receptor signaling pathway / response to psychosocial stress / endosome to lysosome transport / adrenergic receptor signaling pathway / diet induced thermogenesis / positive regulation of protein kinase A signaling / neuronal dense core vesicle / adenylate cyclase binding / smooth muscle contraction / potassium channel regulator activity / bone resorption / positive regulation of bone mineralization / brown fat cell differentiation / adenylate cyclase-activating adrenergic receptor signaling pathway / regulation of sodium ion transport / viral release from host cell by cytolysis / response to cold / peptidoglycan catabolic process / receptor-mediated endocytosis / clathrin-coated endocytic vesicle membrane / positive regulation of protein serine/threonine kinase activity / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / cellular response to amyloid-beta / cell wall macromolecule catabolic process / lysozyme / Cargo recognition for clathrin-mediated endocytosis / lysozyme activity / Clathrin-mediated endocytosis / 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 / early endosome / lysosome / receptor complex / cell surface receptor signaling pathway / 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 / identical protein binding / membrane / nucleus / plasma membrane
Similarity search - Function
Beta 2 adrenoceptor / Adrenoceptor family / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Lysozyme - #40 / Endolysin T4 type / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme ...Beta 2 adrenoceptor / Adrenoceptor family / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Lysozyme - #40 / Endolysin T4 type / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily / Serpentine type 7TM GPCR chemoreceptor Srsx / Lysozyme / 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 / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CHOLESTEROL / Chem-ERC / Endolysin / Beta-2 adrenergic receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Enterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsRosenbaum, D.M. / Zhang, C. / Lyons, J.A. / Holl, R. / Aragao, D. / Arlow, D.H. / Rasmussen, S.G.F. / Choi, H.-J. / DeVree, B.T. / Sunahara, R.K. ...Rosenbaum, D.M. / Zhang, C. / Lyons, J.A. / Holl, R. / Aragao, D. / Arlow, D.H. / Rasmussen, S.G.F. / Choi, H.-J. / DeVree, B.T. / Sunahara, R.K. / Chae, P.S. / Gellman, S.H. / Dror, R.O. / Shaw, D.E. / Weis, W.I. / Caffrey, M. / Gmeiner, P. / Kobilka, B.K.
CitationJournal: Nature / Year: 2011
Title: Structure and function of an irreversible agonist-beta(2) adrenoceptor complex
Authors: Rosenbaum, D.M. / Zhang, C. / Lyons, J.A. / Holl, R. / Aragao, D. / Arlow, D.H. / Rasmussen, S.G.F. / Choi, H.J. / Devree, B.T. / Sunahara, R.K. / Chae, P.S. / Gellman, S.H. / Dror, R.O. / ...Authors: Rosenbaum, D.M. / Zhang, C. / Lyons, J.A. / Holl, R. / Aragao, D. / Arlow, D.H. / Rasmussen, S.G.F. / Choi, H.J. / Devree, B.T. / Sunahara, R.K. / Chae, P.S. / Gellman, S.H. / Dror, R.O. / Shaw, D.E. / Weis, W.I. / Caffrey, M. / Gmeiner, P. / Kobilka, B.K.
History
DepositionOct 24, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Mar 29, 2023Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fusion protein Beta-2 adrenergic receptor/Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8619
Polymers52,4531
Non-polymers1,4088
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)282.440, 40.040, 65.210
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 Fusion protein Beta-2 adrenergic receptor/Lysozyme / Beta-2 adrenoreceptor / Beta-2 adrenoceptor


Mass: 52453.273 Da / Num. of mol.: 1 / Mutation: H93C,N187E,C265A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Enterobacteria phage T4 (virus)
Gene: ADRB2, ADRB2R, B2AR / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P07550, UniProt: P00720, lysozyme
#2: Chemical ChemComp-ERC / 8-hydroxy-5-[(1R)-1-hydroxy-2-({2-[3-methoxy-4-(3-sulfanylpropoxy)phenyl]ethyl}amino)ethyl]quinolin-2(1H)-one / Endolysin / Lysis protein / Muramidase


Mass: 444.544 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H28N2O5S
#3: Chemical ChemComp-CLR / CHOLESTEROL / Beta-2 adrenoreceptor / Beta-2 adrenoceptor


Mass: 386.654 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H46O
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 19

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Sample preparation

CrystalDensity Matthews: 3.51 Å3/Da / Density % sol: 65 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 6.7
Details: 26 %(v/v) PEG 400, 200 mM Li2SO4, 4 %(v/v) DMSO, 3.5 %(v/v) 1,4-butandediol, 100 mM MES pH 6.7, Lipidic Cubic Phase, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 30, 2010
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 3.5→65 Å / Num. all: 10025 / Num. obs: 9385 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.202
Reflection shellResolution: 3.5→3.69 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.443 / Mean I/σ(I) obs: 2 / % possible all: 94

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Processing

Software
NameVersionClassification
JBluIce-EPICSdata collection
PHASERphasing
BUSTER2.8.0refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2RH1

2rh1


Resolution: 3.5→65.21 Å / Cor.coef. Fo:Fc: 0.8466 / Cor.coef. Fo:Fc free: 0.7701 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.283 944 10.09 %RANDOM
Rwork0.238 ---
all0.2407 10025 --
obs0.2407 9352 --
Displacement parametersBiso mean: 81.8 Å2
Baniso -1Baniso -2Baniso -3
1-7.5537 Å20 Å20 Å2
2--14.0671 Å20 Å2
3----21.6208 Å2
Refine analyzeLuzzati coordinate error obs: 0.879 Å
Refinement stepCycle: LAST / Resolution: 3.5→65.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3539 0 89 0 3628
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1240SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes72HARMONIC2
X-RAY DIFFRACTIONt_gen_planes544HARMONIC5
X-RAY DIFFRACTIONt_it3672HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion498SEMIHARMONIC5
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_contact4176SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3708HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg5041HARMONIC20.89
X-RAY DIFFRACTIONt_omega_torsion1.57
X-RAY DIFFRACTIONt_other_torsion20.03
LS refinement shellResolution: 3.5→3.91 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2663 279 11.18 %
Rwork0.2338 2217 -
all0.2375 2496 -
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)
10.8276-0.12860.12331.7725-0.06590.6525-0.03850.1642-0.08350.07410.11150.5950.08640.1853-0.073-0.2547-0.0369-0.01430.05610.02080.389728.52957.57587.4465
21.7561-0.5541-0.52574.10222.91683.4864-0.1886-0.0196-0.0317-0.00280.0146-0.2817-0.03860.13170.174-0.1642-0.0046-0.00070.09210.0722-0.043171.351622.654415.9417
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|29 - A|230 A|263 - A|342 }A29 - 230
2X-RAY DIFFRACTION1{ A|29 - A|230 A|263 - A|342 }A263 - 342
3X-RAY DIFFRACTION2{ A|1002 - A|1161 }A1002 - 1161

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