[English] 日本語
Yorodumi
- PDB-3ny8: Crystal structure of the human beta2 adrenergic receptor in compl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ny8
TitleCrystal structure of the human beta2 adrenergic receptor in complex with the inverse agonist ICI 118,551
ComponentsBeta-2 adrenergic receptor, Lysozyme
KeywordsMEMBRANE PROTEIN / G Protein-coupled receptor / Lysozyme / Fusion / Transducer / Adrenergic / G-Proteins / Arrestins / Adrenalin / ICI 118 / 551 / Glycosylation / Palmitoylation / Phosphorylation / HYDROLASE / Structural Genomics / PSI-2 / Protein Structure Initiative / Accelerated Technologies Center for Gene to 3D Structure / ATCG3D / GPCR Network / GPCR
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 / receptor complex / early endosome / 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 / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Lysozyme - #40 / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / 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 / Lysozyme domain superfamily / Phage lysozyme / Serpentine type 7TM GPCR chemoreceptor Srsx / Lysozyme / 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 / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CHOLESTEROL / Chem-JRZ / OLEIC ACID / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / TRIETHYLENE GLYCOL / Endolysin / Beta-2 adrenergic receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Enterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.84 Å
AuthorsWacker, D. / Fenalti, G. / Brown, M.A. / Katritch, V. / Abagyan, R. / Cherezov, V. / Stevens, R.C. / Accelerated Technologies Center for Gene to 3D Structure (ATCG3D) / GPCR Network (GPCR)
CitationJournal: J.Am.Chem.Soc. / Year: 2010
Title: Conserved Binding Mode of Human beta(2) Adrenergic Receptor Inverse Agonists and Antagonist Revealed by X-ray Crystallography
Authors: Wacker, D. / Fenalti, G. / Brown, M.A. / Katritch, V. / Abagyan, R. / Cherezov, V. / Stevens, R.C.
History
DepositionJul 14, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 23, 2012Group: Database references
Revision 1.3Aug 8, 2012Group: Other
Revision 1.4Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.5Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Beta-2 adrenergic receptor, Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1548
Polymers55,9581
Non-polymers2,1967
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.711, 76.148, 174.207
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Beta-2 adrenergic receptor, Lysozyme / / BETA-2 ADRENORECEPTOR, BETA-2 ADRENOCEPTOR, LYSIS PROTEIN, MURAMIDASE, ENDOLYSIN / BETA-2 ADRENORECEPTOR / BETA-2 ADRENOCEPTOR / LYSIS PROTEIN / MURAMIDASE / ENDOLYSIN


Mass: 55957.926 Da / Num. of mol.: 1
Fragment: Chimeric protein of Beta-2 Adrenoreceptor 1-230, Lysozyme 2-161, Beta-2 adrenergic receptor 263-348
Mutation: E122W, N187E, C1054T, C1097A
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 / Plasmid: PFASTBAC / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: P07550, UniProt: P00720

-
Non-polymers , 6 types, 29 molecules

#2: Chemical ChemComp-CLR / CHOLESTEROL / Cholesterol


Mass: 386.654 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H46O
#3: Chemical ChemComp-JRZ / (2S,3S)-1-[(7-methyl-2,3-dihydro-1H-inden-4-yl)oxy]-3-[(1-methylethyl)amino]butan-2-ol


Mass: 277.402 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H27NO2
#4: Chemical ChemComp-OLA / OLEIC ACID / Oleic acid


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


Mass: 356.540 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H40O4
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O

-
Details

Nonpolymer detailsLIGAND JRZ REFERS TO ICI 118,551

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 9

-
Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 49.02 %
Crystal growTemperature: 293 K
Details: 100 mM Tris/HCl pH 7.5-8.0, 200-500 mM Na-formate, 5% 1,4 butanediol, 27-32% PEG 400, Lipidic Cubic Phase (LCP) Crystallization, temperature 293-295K
PH range: 7.5-8.0

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 23-ID-D11.0332
SYNCHROTRONAPS 23-ID-D21.0332
Detector
TypeIDDetectorDate
MARMOSAIC 300 mm CCD1CCDNov 19, 2009
MARMOSAIC 300 mm CCD2CCDDec 10, 2009
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double CrystalSINGLE WAVELENGTHMx-ray1
2Double CrystalSINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.84→40 Å / Num. all: 13472 / Num. obs: 12177 / % possible obs: 90.4 % / Observed criterion σ(I): -3 / Redundancy: 4.52 % / Rsym value: 0.141 / Net I/σ(I): 8.4
Reflection shellResolution: 2.84→2.99 Å / Redundancy: 3.27 % / Mean I/σ(I) obs: 2.08 / Num. unique all: 1875 / Rsym value: 0.498 / % possible all: 72.4

-
Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.5.0102refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2RH1

2rh1


Resolution: 2.84→37.81 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.887 / SU B: 21.078 / SU ML: 0.409 / Cross valid method: THROUGHOUT / ESU R Free: 0.475 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29073 609 5 %RANDOM
Rwork0.22585 ---
obs0.22912 11566 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.899 Å2
Baniso -1Baniso -2Baniso -3
1-5.84 Å20 Å20 Å2
2---0.97 Å20 Å2
3----4.88 Å2
Refinement stepCycle: LAST / Resolution: 2.84→37.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3527 0 149 22 3698
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223764
X-RAY DIFFRACTIONr_bond_other_d0.0020.022604
X-RAY DIFFRACTIONr_angle_refined_deg1.141.9795101
X-RAY DIFFRACTIONr_angle_other_deg0.87436337
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4725438
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.12323.072153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.02615623
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6981522
X-RAY DIFFRACTIONr_chiral_restr0.0610.2567
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023953
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02793
X-RAY DIFFRACTIONr_mcbond_it0.4231.52182
X-RAY DIFFRACTIONr_mcbond_other0.0471.5889
X-RAY DIFFRACTIONr_mcangle_it0.823542
X-RAY DIFFRACTIONr_scbond_it0.86331582
X-RAY DIFFRACTIONr_scangle_it1.4724.51559
LS refinement shellResolution: 2.84→2.913 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 33 -
Rwork0.304 630 -
obs--100 %

+
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