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- PDB-6ps5: XFEL beta2 AR structure by ligand exchange from Timolol to Propra... -

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Basic information

Entry
Database: PDB / ID: 6ps5
TitleXFEL beta2 AR structure by ligand exchange from Timolol to Propranolol.
ComponentsFusion protein of Beta-2 adrenergic receptor and T4 Lysozyme
KeywordsMEMBRANE PROTEIN / GPCR / COMPLEX-LCP method / SBDD / drug design / XFEL / LCP-SFX / Ligand Exchange / Timolol / Propranolol / b2AR / beta2AR
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 / 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 ...Beta 2 adrenoceptor / Adrenoceptor family / 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
Similarity search - Domain/homology
CHOLESTEROL / OLEIC ACID / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-(ISOPROPYLAMINO)-3-(1-NAPHTHYLOXY)-2-PROPANOL / Endolysin / Beta-2 adrenergic receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Enterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.9 Å
AuthorsIshchenko, A. / Stauch, B. / Han, G.W. / Batyuk, A. / Shiriaeva, A. / Li, C. / Zatsepin, N.A. / Weierstall, U. / Liu, W. / Nango, E. ...Ishchenko, A. / Stauch, B. / Han, G.W. / Batyuk, A. / Shiriaeva, A. / Li, C. / Zatsepin, N.A. / Weierstall, U. / Liu, W. / Nango, E. / Nakane, T. / Tanaka, R. / Tono, K. / Joti, Y. / Iwata, S. / Moraes, I. / Gati, C. / Cherezov, C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM127086 United States
CitationJournal: Iucrj / Year: 2019
Title: Toward G protein-coupled receptor structure-based drug design using X-ray lasers.
Authors: Ishchenko, A. / Stauch, B. / Han, G.W. / Batyuk, A. / Shiriaeva, A. / Li, C. / Zatsepin, N. / Weierstall, U. / Liu, W. / Nango, E. / Nakane, T. / Tanaka, R. / Tono, K. / Joti, Y. / Iwata, S. ...Authors: Ishchenko, A. / Stauch, B. / Han, G.W. / Batyuk, A. / Shiriaeva, A. / Li, C. / Zatsepin, N. / Weierstall, U. / Liu, W. / Nango, E. / Nakane, T. / Tanaka, R. / Tono, K. / Joti, Y. / Iwata, S. / Moraes, I. / Gati, C. / Cherezov, V.
History
DepositionJul 12, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fusion protein of Beta-2 adrenergic receptor and T4 Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,79613
Polymers57,7741
Non-polymers3,02112
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.730, 77.600, 173.880
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsAUTHORS STATE THAT THE BIOLOGICAL UNIT IS UNKNOWN

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Fusion protein of Beta-2 adrenergic receptor and T4 Lysozyme / / Beta-2 adrenoreceptor / Beta-2 adrenoceptor / Lysis protein / Lysozyme / Muramidase


Mass: 57774.246 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Enterobacteria phage T4 (virus)
Gene: ADRB2, ADRB2R, B2AR, e, T4Tp126 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P07550, UniProt: D9IEF7

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Non-polymers , 5 types, 12 molecules

#2: Chemical ChemComp-SNP / 1-(ISOPROPYLAMINO)-3-(1-NAPHTHYLOXY)-2-PROPANOL / S-PROPRANOLOL


Mass: 259.343 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H21NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CLR / CHOLESTEROL / Cholesterol


Mass: 386.654 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H46O
#5: Chemical ChemComp-OLA / OLEIC ACID / Oleic acid


Mass: 282.461 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H34O2
#6: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H40O4

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Details

Has ligand of interestY

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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: 2.49 Å3/Da / Density % sol: 50.7 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 0.1 M HEPES pH 7.0, 0.1 M Ammonium Sulfate, 30% PEG 400, 2 mM of target ligand Propranolol

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL3 / Wavelength: 1.76 Å
DetectorType: MPCCD / Detector: CCD / Date: May 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.76 Å / Relative weight: 1
ReflectionResolution: 2.9→46.44 Å / Num. obs: 13464 / % possible obs: 100 % / Redundancy: 104 % / CC1/2: 0.961 / R split: 0.233 / Net I/σ(I): 2.8
Reflection shellResolution: 2.9→3.13 Å / Num. unique obs: 2674 / CC1/2: 0.225 / R split: 1.854
Serial crystallography measurementCollection time total: 1.08 hours / Focal spot size: 1.5 µm2 / Pulse duration: 10 fsec. / Pulse photon energy: 7 keV / XFEL pulse repetition rate: 30 Hz
Serial crystallography sample deliveryMethod: injection
Serial crystallography data reductionCrystal hits: 8494 / Frames indexed: 5201 / Frames total: 117972

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHASERphasing
BUSTER2.10.2refinement
PDB_EXTRACT3.25data extraction
CrystFELdata reduction
CrystFELdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3d4s

3d4s


Resolution: 2.9→46.44 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.91 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.384
RfactorNum. reflection% reflectionSelection details
Rfree0.258 673 5.02 %RANDOM
Rwork0.221 ---
obs0.223 13418 99.5 %-
Displacement parametersBiso max: 186.23 Å2 / Biso mean: 105.25 Å2 / Biso min: 76.13 Å2
Baniso -1Baniso -2Baniso -3
1--7.1817 Å20 Å20 Å2
2--9.3681 Å20 Å2
3----2.1865 Å2
Refine analyzeLuzzati coordinate error obs: 0.52 Å
Refinement stepCycle: final / Resolution: 2.9→46.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3466 0 155 0 3621
Biso mean--118.57 --
Num. residues----442
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1679SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes67HARMONIC2
X-RAY DIFFRACTIONt_gen_planes531HARMONIC5
X-RAY DIFFRACTIONt_it3698HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion497SEMIHARMONIC5
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_contact4031SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3698HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg5023HARMONIC20.92
X-RAY DIFFRACTIONt_omega_torsion1.78
X-RAY DIFFRACTIONt_other_torsion2.82
LS refinement shellResolution: 2.9→3.13 Å / Rfactor Rfree error: 0 / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.239 136 5.13 %
Rwork0.229 2513 -
all0.229 2649 -
obs--97.68 %
Refinement TLS params.Method: refined / Origin x: 8.4218 Å / Origin y: 3.0831 Å / Origin z: 26.0663 Å
111213212223313233
T0.0901 Å20.0142 Å20.011 Å2--0.2011 Å20.0212 Å2---0.3044 Å2
L0.6061 °2-0.2455 °2-0.8568 °2-0.5919 °20.6758 °2--2.7059 °2
S0.0184 Å °-0.0389 Å °0.0123 Å °0.0452 Å °-0.0333 Å °-0.0357 Å °-0.2207 Å °0.0232 Å °0.0149 Å °
Refinement TLS groupSelection details: { A|* }

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