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- PDB-8w1v: The beta2 adrenergic receptor bound to a bitopic ligand -

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Basic information

Entry
Database: PDB / ID: 8w1v
TitleThe beta2 adrenergic receptor bound to a bitopic ligand
Components
  • Beta-2 adrenergic receptor,Endolysin
  • Nanobody60
KeywordsMEMBRANE PROTEIN / signal transduction / bitopic ligand / / SIGNALING PROTEIN / GPCR
Function / homology
Function and homology information


positive regulation of mini excitatory postsynaptic potential / beta2-adrenergic receptor activity / AMPA selective glutamate receptor signaling pathway / norepinephrine binding / positive regulation of autophagosome maturation / norepinephrine-epinephrine-mediated vasodilation involved in regulation of systemic arterial blood pressure / heat generation / Adrenoceptors / activation of transmembrane receptor protein tyrosine kinase activity / negative regulation of smooth muscle contraction ...positive regulation of mini excitatory postsynaptic potential / beta2-adrenergic receptor activity / AMPA selective glutamate receptor signaling pathway / norepinephrine binding / positive regulation of autophagosome maturation / norepinephrine-epinephrine-mediated vasodilation involved in regulation of systemic arterial blood pressure / heat generation / Adrenoceptors / activation of transmembrane receptor protein tyrosine kinase activity / negative regulation of smooth muscle contraction / positive regulation of lipophagy / negative regulation of G protein-coupled receptor signaling pathway / negative regulation of multicellular organism growth / adrenergic receptor signaling pathway / response to psychosocial stress / endosome to lysosome transport / diet induced thermogenesis / neuronal dense core vesicle / positive regulation of cAMP/PKA signal transduction / adenylate cyclase binding / smooth muscle contraction / bone resorption / positive regulation of bone mineralization / potassium channel regulator activity / brown fat cell differentiation / intercellular bridge / viral release from host cell by cytolysis / regulation of sodium ion transport / adenylate cyclase-activating adrenergic receptor signaling pathway / peptidoglycan catabolic process / 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 / cell wall macromolecule catabolic process / mitotic spindle / lysozyme / lysozyme activity / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / amyloid-beta binding / positive regulation of cold-induced thermogenesis / microtubule cytoskeleton / G alpha (s) signalling events / transcription by RNA polymerase II / host cell cytoplasm / early endosome / lysosome / receptor complex / cell surface receptor signaling pathway / positive regulation of MAPK cascade / endosome / endosome membrane / Ub-specific processing proteases / ciliary basal body / defense response to bacterium / cilium / 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 / Endolysin T4 type / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. ...Beta 2 adrenoceptor / Adrenoceptor family / Endolysin T4 type / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. / Lysozyme-like domain superfamily / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family)
Similarity search - Domain/homology
: / Lauryl Maltose Neopentyl Glycol / Endolysin / Beta-2 adrenergic receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsGaiser, B. / Danielsen, M. / Xu, X. / Jorgensen, K. / Fronik, P. / Marcher-Rorsted, E. / Wrobe, T. / Hirata, K. / Liu, X. / Mathiesen, J. / Pedersen, D.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)Grant 32122041 China
CitationJournal: J.Med.Chem. / Year: 2024
Title: Bitopic Ligands Support the Presence of a Metastable Binding Site at the beta 2 Adrenergic Receptor.
Authors: Gaiser, B.I. / Danielsen, M. / Xu, X. / Ropke Jorgensen, K. / Fronik, P. / Marcher-Rorsted, E. / Wrobel, T.M. / Liu, X. / Mosolff Mathiesen, J. / Sejer Pedersen, D.
History
DepositionFeb 19, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2024Group: 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 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _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,Endolysin
B: Beta-2 adrenergic receptor,Endolysin
D: Nanobody60
F: Nanobody60
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,6497
Polymers151,4804
Non-polymers2,1693
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.680, 146.770, 91.830
Angle α, β, γ (deg.)90.000, 107.060, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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


Mass: 62208.852 Da / Num. of mol.: 2 / Mutation: N187E,C1054T,C1097A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADRB2, ADRB2R, B2AR / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P07550, UniProt: P00720, lysozyme
#2: Antibody Nanobody60


Mass: 13531.025 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Spodoptera frugiperda (fall armyworm)
#3: Chemical ChemComp-A1AE2 / (2S)-1-[(3-{1-[4-(4-{(2S)-2-hydroxy-3-[(propan-2-yl)amino]propoxy}phenyl)butyl]-1H-1,2,3-triazol-4-yl}propyl)amino]-3-(2-propylphenoxy)propan-2-ol


Mass: 581.789 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H51N5O4
#4: Chemical ChemComp-AV0 / Lauryl Maltose Neopentyl Glycol / 2,2-didecylpropane-1,3-bis-b-D-maltopyranoside / 2-decyl-2-{[(4-O-alpha-D-glucopyranosyl-beta-D-glucopyranosyl)oxy]methyl}dodecyl4-O-alpha-D-glucopyranosyl-beta-D-glucopyranoside


Mass: 1005.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C47H88O22 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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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: 3.29 Å3/Da / Density % sol: 62.57 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 100 mM Tris buffer (pH 8.0), 100 to 175 mM lithium sulfate, 38% to 42% PEG400, and 10 mM EDTA

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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: Jul 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.92→48.44 Å / Num. obs: 40547 / % possible obs: 99.9 % / Redundancy: 55.5 % / Biso Wilson estimate: 54.78 Å2 / CC1/2: 0.984 / Net I/σ(I): 8.25
Reflection shellResolution: 3→3.1 Å / Num. unique obs: 6655 / CC1/2: 0.564

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→48.44 Å / SU ML: 0.4897 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.5555
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2919 2068 5.54 %
Rwork0.2477 35291 -
obs0.2501 37359 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.43 Å2
Refinement stepCycle: LAST / Resolution: 3→48.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8760 0 153 0 8913
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00719106
X-RAY DIFFRACTIONf_angle_d0.70512348
X-RAY DIFFRACTIONf_chiral_restr0.04341429
X-RAY DIFFRACTIONf_plane_restr0.00431509
X-RAY DIFFRACTIONf_dihedral_angle_d14.87863188
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.070.44211330.36062351X-RAY DIFFRACTION99.72
3.07-3.150.37521340.3272345X-RAY DIFFRACTION99.84
3.15-3.230.35311370.3112347X-RAY DIFFRACTION99.84
3.23-3.330.32991350.27772356X-RAY DIFFRACTION99.92
3.33-3.430.30571400.26652337X-RAY DIFFRACTION100
3.43-3.560.28891390.25822329X-RAY DIFFRACTION99.88
3.56-3.70.311370.24272369X-RAY DIFFRACTION100
3.7-3.870.2871450.23322330X-RAY DIFFRACTION100
3.87-4.070.23591280.22242350X-RAY DIFFRACTION100
4.07-4.330.25861420.21212374X-RAY DIFFRACTION100
4.33-4.660.28331380.22012330X-RAY DIFFRACTION100
4.66-5.130.27311420.23242355X-RAY DIFFRACTION99.84
5.13-5.870.32461400.26652358X-RAY DIFFRACTION99.96
5.87-7.390.27851360.26682377X-RAY DIFFRACTION100
7.39-48.440.25131420.21622383X-RAY DIFFRACTION99.49

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