[English] 日本語
Yorodumi
- PDB-6ps2: XFEL beta2 AR structure by ligand exchange from Timolol to Alprenolol. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ps2
TitleXFEL beta2 AR structure by ligand exchange from Timolol to Alprenolol.
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 / Alprenolol / b2AR / beta2AR
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 / response to psychosocial stress / adrenergic receptor signaling pathway / diet induced thermogenesis / positive regulation of cAMP/PKA signal transduction / adenylate cyclase binding / smooth muscle contraction / bone resorption / positive regulation of bone mineralization / potassium channel regulator activity / 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 membrane / endosome / 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 / 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
CHOLESTEROL / Chem-JTZ / OLEIC ACID / (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 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: 2.4 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
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)63,49021
Polymers57,7741
Non-polymers5,71520
Water64936
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.650, 76.240, 171.900
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

-
Components

-
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

-
Non-polymers , 7 types, 56 molecules

#2: Chemical ChemComp-JTZ / (2S)-1-[(1-methylethyl)amino]-3-(2-prop-2-en-1-ylphenoxy)propan-2-ol


Mass: 249.349 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H46O
#4: Chemical
ChemComp-OLB / (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate


Mass: 356.540 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C21H40O4
#5: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H40O4
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#7: Chemical
ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H34O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.22 %
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 Alprenolol

-
Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.33 Å
DetectorType: CS-PAD CXI-1 / Detector: PIXEL / Date: Nov 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.33 Å / Relative weight: 1
ReflectionResolution: 2.4→30.82 Å / Num. obs: 22282 / % possible obs: 100 % / Redundancy: 503.6 % / CC1/2: 0.994 / R split: 0.089 / Net I/σ(I): 6.2
Reflection shellResolution: 2.4→2.52 Å / Num. unique obs: 2944 / CC1/2: 0.296 / R split: 2.063
Serial crystallography measurementCollection time total: 1.8 hours / Focal spot size: 1.5 µm2 / Pulse duration: 42 fsec. / Pulse photon energy: 9.5 keV / XFEL pulse repetition rate: 120 Hz
Serial crystallography sample deliveryMethod: injection
Serial crystallography sample delivery injectionFlow rate: 0.2 µL/min / Injector diameter: 50 µm
Serial crystallography data reductionCrystal hits: 99984 / Frames indexed: 60694 / Frames total: 775070

-
Phasing

PhasingMethod: molecular replacement

-
Processing

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

3d4s


Resolution: 2.4→30.82 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.944 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.33 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.331 / SU Rfree Blow DPI: 0.222 / SU Rfree Cruickshank DPI: 0.224
RfactorNum. reflection% reflectionSelection details
Rfree0.224 1110 5 %RANDOM
Rwork0.181 ---
obs0.183 22205 99.9 %-
Displacement parametersBiso max: 185.2 Å2 / Biso mean: 89.28 Å2 / Biso min: 53.62 Å2
Baniso -1Baniso -2Baniso -3
1--13.7622 Å20 Å20 Å2
2--5.2428 Å20 Å2
3---8.5195 Å2
Refine analyzeLuzzati coordinate error obs: 0.36 Å
Refinement stepCycle: final / Resolution: 2.4→30.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3526 0 266 36 3828
Biso mean--113.2 81.72 -
Num. residues----443
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1832SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes72HARMONIC2
X-RAY DIFFRACTIONt_gen_planes562HARMONIC5
X-RAY DIFFRACTIONt_it3920HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion505SEMIHARMONIC5
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_contact4779SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3920HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg5291HARMONIC21.03
X-RAY DIFFRACTIONt_omega_torsion2.64
X-RAY DIFFRACTIONt_other_torsion3.28
LS refinement shellResolution: 2.4→2.52 Å / Rfactor Rfree error: 0 / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.282 142 4.96 %
Rwork0.247 2722 -
all0.249 2864 -
obs--99.34 %
Refinement TLS params.Method: refined / Origin x: 8.7183 Å / Origin y: 3.6358 Å / Origin z: 25.9184 Å
111213212223313233
T0.0114 Å2-0.0237 Å2-0.023 Å2--0.2651 Å20.0355 Å2---0.275 Å2
L0.8897 °2-0.4335 °2-0.8596 °2-0.8853 °20.6668 °2--2.8863 °2
S-0.0249 Å °0.0024 Å °0.0524 Å °0.1198 Å °-0.0148 Å °-0.0586 Å °-0.2753 Å °0.0889 Å °0.0398 Å °
Refinement TLS groupSelection details: { A|* }

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more