[English] 日本語
Yorodumi
- PDB-6rz6: Crystal structure of the human cysteinyl leukotriene receptor 2 i... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6rz6
TitleCrystal structure of the human cysteinyl leukotriene receptor 2 in complex with ONO-2570366 (C2221 space group)
ComponentsCysteinyl leukotriene receptor 2,Soluble cytochrome b562,Cysteinyl leukotriene receptor 2
KeywordsMEMBRANE PROTEIN / GPCR / LCP / cysteinyl leukotriene / cyslt2 / cysltr2 / cyslt2r / asthma / BRIL / Cysteinyl Leukotriene Receptor 2
Function / homology
Function and homology information


cysteinyl leukotriene receptor activity / leukotriene receptor activity / Leukotriene receptors / LTC4-CYSLTR mediated IL4 production / G protein-coupled peptide receptor activity / neuropeptide signaling pathway / G alpha (s) signalling events / G alpha (q) signalling events / electron transfer activity / periplasmic space ...cysteinyl leukotriene receptor activity / leukotriene receptor activity / Leukotriene receptors / LTC4-CYSLTR mediated IL4 production / G protein-coupled peptide receptor activity / neuropeptide signaling pathway / G alpha (s) signalling events / G alpha (q) signalling events / electron transfer activity / periplasmic space / immune response / iron ion binding / heme binding / plasma membrane
Similarity search - Function
Cysteinyl leukotriene receptor 2 / Cysteinyl leukotriene receptor / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / 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-KNW / OLEIC ACID / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / L(+)-TARTARIC ACID / Soluble cytochrome b562 / Cysteinyl leukotriene receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsGusach, A. / Luginina, A. / Marin, E. / Brouillette, R.L. / Besserer-Offroy, E. / Longpre, J.M. / Ishchenko, A. / Popov, P. / Fujimoto, T. / Maruyama, T. ...Gusach, A. / Luginina, A. / Marin, E. / Brouillette, R.L. / Besserer-Offroy, E. / Longpre, J.M. / Ishchenko, A. / Popov, P. / Fujimoto, T. / Maruyama, T. / Stauch, B. / Ergasheva, M. / Romanovskaya, D. / Stepko, A. / Kovalev, K. / Shevtsov, M. / Gordeliy, V. / Han, G.W. / Sarret, P. / Katritch, V. / Borshchevskiy, V. / Mishin, A. / Cherezov, V.
Funding support Russian Federation, United States, Canada, 4items
OrganizationGrant numberCountry
Russian Science Foundation16-14-10273 Russian Federation
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM127086 United States
Canadian Institutes of Health Research Canada
Fonds de Recherche du Quebec - Nature et Technologies Canada
CitationJournal: Nat Commun / Year: 2019
Title: Structural basis of ligand selectivity and disease mutations in cysteinyl leukotriene receptors.
Authors: Gusach, A. / Luginina, A. / Marin, E. / Brouillette, R.L. / Besserer-Offroy, E. / Longpre, J.M. / Ishchenko, A. / Popov, P. / Patel, N. / Fujimoto, T. / Maruyama, T. / Stauch, B. / ...Authors: Gusach, A. / Luginina, A. / Marin, E. / Brouillette, R.L. / Besserer-Offroy, E. / Longpre, J.M. / Ishchenko, A. / Popov, P. / Patel, N. / Fujimoto, T. / Maruyama, T. / Stauch, B. / Ergasheva, M. / Romanovskaia, D. / Stepko, A. / Kovalev, K. / Shevtsov, M. / Gordeliy, V. / Han, G.W. / Katritch, V. / Borshchevskiy, V. / Sarret, P. / Mishin, A. / Cherezov, V.
History
DepositionJun 12, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 11, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Database references / Category: 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 1.2Mar 30, 2022Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / entity / pdbx_audit_support / pdbx_entity_nonpoly
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_audit_support.funding_organization / _pdbx_entity_nonpoly.name
Revision 1.3Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cysteinyl leukotriene receptor 2,Soluble cytochrome b562,Cysteinyl leukotriene receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,88531
Polymers45,9961
Non-polymers9,88930
Water63135
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: BIOLOGICAL UNIT IS UNKNOWN
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6080 Å2
ΔGint24 kcal/mol
Surface area19770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.810, 170.880, 85.790
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Cysteinyl leukotriene receptor 2,Soluble cytochrome b562,Cysteinyl leukotriene receptor 2 / CysLTR2 / G-protein coupled receptor GPCR21 / hGPCR21 / G-protein coupled receptor HG57 / HPN321 / ...CysLTR2 / G-protein coupled receptor GPCR21 / hGPCR21 / G-protein coupled receptor HG57 / HPN321 / Cytochrome b-562 / CysLTR2 / G-protein coupled receptor GPCR21 / hGPCR21 / G-protein coupled receptor HG57 / HPN321


Mass: 45995.961 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Escherichia coli (E. coli)
Gene: CYSLTR2, CYSLT2, CYSLT2R, PSEC0146, cybC / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9NS75, UniProt: P0ABE7

-
Non-polymers , 7 types, 65 molecules

#2: Chemical ChemComp-KNW / (2~{S})-8-[[4-[4-(2-chloranyl-5-fluoranyl-phenyl)butoxy]phenyl]carbonylamino]-4-(4-oxidanyl-4-oxidanylidene-butyl)-2,3- dihydro-1,4-benzoxazine-2-carboxylic acid / ONO-2570366


Mass: 585.020 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H30ClFN2O7 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CLR / CHOLESTEROL / Cholesterol


Mass: 386.654 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H46O
#4: Chemical ChemComp-TLA / L(+)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#5: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C21H40O4
#6: Chemical
ChemComp-OLA / OLEIC ACID / Oleic acid


Mass: 282.461 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C18H34O2
#7: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.81 Å3/Da / Density % sol: 56 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 8
Details: 100-200 mM NH4 Tartrate dibasic 28-32% v/v PEG400 100 mM HEPES pH 8.0

-
Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21001N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID2911.07228
SYNCHROTRONESRF ID30B20.97625
Detector
TypeIDDetectorDate
DECTRIS PILATUS3 6M1PIXELApr 22, 2017
DECTRIS PILATUS3 S 6M2PIXELApr 22, 2017
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.072281
20.976251
ReflectionResolution: 2.43→30 Å / Num. obs: 19685 / % possible obs: 99.8 % / Redundancy: 9.2 % / Biso Wilson estimate: 51.5 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.279 / Rpim(I) all: 0.094 / Net I/σ(I): 5.9
Reflection shellResolution: 2.43→2.52 Å / Redundancy: 8.8 % / Rmerge(I) obs: 3.23 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1945 / CC1/2: 0.3 / Rpim(I) all: 1.12 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
PHENIX1.12-2829refinement
XDS20161205data reduction
XSCALE20180319data scaling
PHASER1.12-2829phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6RZ4

6rz4


Resolution: 2.43→28.901 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.52
RfactorNum. reflection% reflection
Rfree0.2321 982 4.99 %
Rwork0.1944 --
obs0.1964 19660 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.43→28.901 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2770 0 493 35 3298
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063328
X-RAY DIFFRACTIONf_angle_d1.0224401
X-RAY DIFFRACTIONf_dihedral_angle_d11.7853122
X-RAY DIFFRACTIONf_chiral_restr0.056503
X-RAY DIFFRACTIONf_plane_restr0.007515
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.43-2.55810.32351370.27132614X-RAY DIFFRACTION100
2.5581-2.71820.29661390.25122634X-RAY DIFFRACTION100
2.7182-2.92790.2941390.21952635X-RAY DIFFRACTION100
2.9279-3.22220.26171400.2182658X-RAY DIFFRACTION100
3.2222-3.68770.21461390.19352676X-RAY DIFFRACTION100
3.6877-4.6430.17981430.15832686X-RAY DIFFRACTION100
4.643-28.90290.24311450.19032775X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.51580.2438-0.14880.6588-0.08411.6887-0.03960.17480.0527-0.13170.0354-0.070.0229-0.1-0.01620.26550.00310.00710.402-0.01870.3026-19.33442.1588-21.8558
22.10421.1356-2.11287.8899-0.00463.41020.01710.1655-0.6559-0.72670.5593-0.14431.96810.1039-0.64171.39820.0579-0.16430.6634-0.0740.7746-18.3203-42.87520.968
32.0110.0521-0.22262.0622-0.0031.7677-0.07290.0036-0.01360.09750.0521-0.2210.03670.1063-0.00440.2811-0.0219-0.01240.39790.00850.2785-14.93121.491-13.9613
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 29 through 232)
2X-RAY DIFFRACTION2(chain 'A' and resid 1001 through 1106)
3X-RAY DIFFRACTION3(chain 'A' and resid 240 through 322)

+
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