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- PDB-7xka: Structure of human beta2 adrenergic receptor bound to constrained... -

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Basic information

Entry
Database: PDB / ID: 7xka
TitleStructure of human beta2 adrenergic receptor bound to constrained epinephrine
Components
  • Camelid Antibody Fragment
  • Endolysin,Beta-2 adrenergic receptor
KeywordsMEMBRANE PROTEIN / GPCR
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) / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Chem-G1I / Endolysin / Beta-2 adrenergic receptor
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsXu, X. / Shonberg, J. / Kaindl, J. / Clark, M. / Stobel, A. / Maul, L. / Mayer, D. / Hubner, H. / Venkatakrishnan, A. / Dror, R. ...Xu, X. / Shonberg, J. / Kaindl, J. / Clark, M. / Stobel, A. / Maul, L. / Mayer, D. / Hubner, H. / Venkatakrishnan, A. / Dror, R. / Kobilka, B.K. / Sunahara, R. / Liu, X. / Gmeiner, P.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2023
Title: Constrained catecholamines gain beta 2 AR selectivity through allosteric effects on pocket dynamics.
Authors: Xu, X. / Shonberg, J. / Kaindl, J. / Clark, M.J. / Stossel, A. / Maul, L. / Mayer, D. / Hubner, H. / Hirata, K. / Venkatakrishnan, A.J. / Dror, R.O. / Kobilka, B.K. / Sunahara, R.K. / Liu, X. / Gmeiner, P.
History
DepositionApr 19, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 26, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.3Oct 23, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)66,6534
Polymers66,4202
Non-polymers2322
Water181
1
A: Endolysin,Beta-2 adrenergic receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7033
Polymers53,4711
Non-polymers2322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-12 kcal/mol
Surface area24080 Å2
MethodPISA
2
B: Camelid Antibody Fragment


Theoretical massNumber of molelcules
Total (without water)12,9491
Polymers12,9491
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.600, 66.560, 302.720
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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


Mass: 53471.039 Da / Num. of mol.: 1 / Mutation: C918T,C962A,M1096T,M1098T,N1157E,C1265A
Source method: isolated from a genetically manipulated source
Details: Chimera protein
Source: (gene. exp.) Enterobacteria phage T4, (gene. exp.) Homo sapiens (human)
Gene: ADRB2, ADRB2R, B2AR / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P00720, UniProt: P07550, lysozyme
#2: Antibody Camelid Antibody Fragment


Mass: 12949.375 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)
#3: Chemical ChemComp-G1I / (5R,6R)-6-(methylamino)-5,6,7,8-tetrahydronaphthalene-1,2,5-triol


Mass: 209.242 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H15NO3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
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: 3.87 Å3/Da / Density % sol: 68.21 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 100mM Tris-HCl, pH 8.0, 150-200mM 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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→19.96 Å / Num. obs: 18898 / % possible obs: 98.96 % / Redundancy: 11.3 % / Biso Wilson estimate: 66.45 Å2 / CC1/2: 0.983 / Net I/σ(I): 6.73
Reflection shellResolution: 3.1→3.2 Å / Num. unique obs: 1618 / CC1/2: 0.598 / % possible all: 97.2

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4LDE

4lde


Resolution: 3.1→19.96 Å / SU ML: 0.5325 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.5997
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2724 1858 9.84 %
Rwork0.2264 17028 -
obs0.2309 18886 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.25 Å2
Refinement stepCycle: LAST / Resolution: 3.1→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4507 0 16 1 4524
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00294622
X-RAY DIFFRACTIONf_angle_d0.53936284
X-RAY DIFFRACTIONf_chiral_restr0.0389723
X-RAY DIFFRACTIONf_plane_restr0.0031784
X-RAY DIFFRACTIONf_dihedral_angle_d13.3527626
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.180.45811140.37591255X-RAY DIFFRACTION96.89
3.18-3.280.40511360.33831265X-RAY DIFFRACTION98.94
3.28-3.380.34311440.29361276X-RAY DIFFRACTION99.44
3.38-3.50.34621460.27611304X-RAY DIFFRACTION99.66
3.5-3.640.31131430.26441275X-RAY DIFFRACTION99.93
3.64-3.810.33541400.25831311X-RAY DIFFRACTION99.86
3.81-4.010.26751420.22191278X-RAY DIFFRACTION99.93
4.01-4.250.26971460.20861314X-RAY DIFFRACTION100
4.25-4.580.21911490.19741332X-RAY DIFFRACTION100
4.58-5.030.25111450.20061307X-RAY DIFFRACTION99.79
5.03-5.750.25651460.21391328X-RAY DIFFRACTION99.73
5.75-7.180.28391490.22841365X-RAY DIFFRACTION99.93
7.18-19.960.18751580.16281418X-RAY DIFFRACTION99.12

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