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- PDB-6n48: Structure of beta2 adrenergic receptor bound to BI167107, Nanobod... -

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Basic information

Entry
Database: PDB / ID: 6n48
TitleStructure of beta2 adrenergic receptor bound to BI167107, Nanobody 6B9, and a positive allosteric modulator
Components
  • Camelid Antibody Fragment
  • Endolysin,Beta-2 adrenergic receptor,Beta-2 adrenergic receptor chimera
KeywordsSIGNALING PROTEIN / G protein coupled receptor / membrane protein
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 / adrenergic receptor signaling pathway / response to psychosocial stress / diet induced thermogenesis / positive regulation of cAMP/PKA signal transduction / adenylate cyclase binding / smooth muscle contraction / bone resorption / potassium channel regulator activity / positive regulation of bone mineralization / neuronal dense core vesicle / brown fat cell differentiation / viral release from host cell by cytolysis / intercellular bridge / 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 / positive regulation of cold-induced thermogenesis / amyloid-beta binding / microtubule cytoskeleton / G alpha (s) signalling events / transcription by RNA polymerase II / host cell cytoplasm / early endosome / cell surface receptor signaling pathway / lysosome / receptor complex / endosome / endosome membrane / positive regulation of MAPK cascade / Ub-specific processing proteases / defense response to bacterium / 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 / 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. / 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) / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
(2S)-2,3-dihydroxypropyl (7Z)-tetradec-7-enoate / Chem-KBY / Chem-P0G / Endolysin / Beta-2 adrenergic receptor
Similarity search - Component
Biological speciesEnterobacteria phage RB59 (virus)
Homo sapiens (human)
Camelidae (mammal)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsLiu, X. / Masoudi, A. / Kahsai, A.W. / Huang, L.Y. / Pani, B. / Hirata, K. / Ahn, S. / Lefkowitz, R.J. / Kobilka, B.K.
CitationJournal: Science / Year: 2019
Title: Mechanism of beta2AR regulation by an intracellular positive allosteric modulator.
Authors: Liu, X. / Masoudi, A. / Kahsai, A.W. / Huang, L.Y. / Pani, B. / Staus, D.P. / Shim, P.J. / Hirata, K. / Simhal, R.K. / Schwalb, A.M. / Rambarat, P.K. / Ahn, S. / Lefkowitz, R.J. / Kobilka, B.
History
DepositionNov 17, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jul 10, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
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
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)67,7615
Polymers66,4202
Non-polymers1,3413
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint-18 kcal/mol
Surface area28290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.150, 66.060, 303.510
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 Endolysin,Beta-2 adrenergic receptor,Beta-2 adrenergic receptor chimera / Lysis protein / Lysozyme / Muramidase / Beta-2 adrenoreceptor / Beta-2 adrenoceptor


Mass: 53471.039 Da / Num. of mol.: 1
Fragment: chimera of lysozyme and B2AR (UNP residues 29-234,263-348)
Mutation: M1096T, M1098T, N1187E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage RB59 (virus), (gene. exp.) Homo sapiens (human)
Gene: e, RB59_126, ADRB2, ADRB2R, B2AR / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A097J809, UniProt: P07550, lysozyme
#2: Antibody Camelid Antibody Fragment / Nanobody 6B9


Mass: 12949.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelidae (mammal) / Production host: Escherichia coli BL21(DE3) (bacteria)
#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
#4: Chemical ChemComp-1WV / (2S)-2,3-dihydroxypropyl (7Z)-tetradec-7-enoate


Mass: 300.434 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H32O4
#5: Chemical ChemComp-KBY / N-[(3R)-4-(4-tert-butylphenyl)-3-({2-[(4-methoxyphenyl)sulfanyl]-5-[methyl(propan-2-yl)sulfamoyl]benzene-1-carbonyl}amino)butanoyl]glycine


Mass: 669.851 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H43N3O7S2
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: 3.72 Å3/Da / Density % sol: 66.94 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 8
Details: 100 mM Tris-HCl, pH 8.0, 150-200 mM lithium acetate, 43-45% PEG400

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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, 2018
RadiationMonochromator: liquid nitrogen-cooled double crystal Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→48 Å / Num. obs: 16912 / % possible obs: 98.4 % / Redundancy: 31.35 % / CC1/2: 0.986 / Net I/σ(I): 8.95
Reflection shellResolution: 3.2→3.3 Å / Redundancy: 11.1 % / Mean I/σ(I) obs: 1.04 / Num. unique obs: 1380 / CC1/2: 0.584 / % possible all: 91.3

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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 4LDE

4lde


Resolution: 3.2→19.921 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2739 1645 9.79 %
Rwork0.2506 --
obs0.2529 16810 98.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2→19.921 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4497 0 88 0 4585
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044689
X-RAY DIFFRACTIONf_angle_d0.6196379
X-RAY DIFFRACTIONf_dihedral_angle_d7.7272704
X-RAY DIFFRACTIONf_chiral_restr0.067724
X-RAY DIFFRACTIONf_plane_restr0.004791
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2001-3.29380.39651350.37721180X-RAY DIFFRACTION91
3.2938-3.39970.34331160.34431117X-RAY DIFFRACTION93
3.3997-3.52050.36941400.32021249X-RAY DIFFRACTION97
3.5205-3.66060.3121350.30631230X-RAY DIFFRACTION99
3.6606-3.82610.30061360.27591269X-RAY DIFFRACTION100
3.8261-4.02630.25811370.25471257X-RAY DIFFRACTION100
4.0263-4.27620.23781340.23781265X-RAY DIFFRACTION100
4.2762-4.60260.26591400.22061288X-RAY DIFFRACTION100
4.6026-5.05890.27431390.22841295X-RAY DIFFRACTION100
5.0589-5.77530.28331380.2441285X-RAY DIFFRACTION100
5.7753-7.21830.23581430.24521333X-RAY DIFFRACTION100
7.2183-19.92190.21971520.19491397X-RAY DIFFRACTION100

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