[English] 日本語
Yorodumi
- PDB-6n48: Structure of beta2 adrenergic receptor bound to BI167107, Nanobod... -

+
Open data


ID or keywords:

Loading...

-
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


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 / neuronal dense core vesicle / diet induced thermogenesis / 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 / response to cold / receptor-mediated endocytosis / 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 / lysozyme activity / Clathrin-mediated endocytosis / positive regulation of cold-induced thermogenesis / amyloid-beta binding / G alpha (s) signalling events / host cell cytoplasm / transcription by RNA polymerase II / positive regulation of MAPK cascade / 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 / 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
(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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water0
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

-
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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
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