[English] 日本語
Yorodumi
- PDB-2jm5: Solution Structure of the RGS domain from human RGS18 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2jm5
TitleSolution Structure of the RGS domain from human RGS18
ComponentsRegulator of G-protein signaling 18
KeywordsSIGNALING PROTEIN / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


regulation of G protein-coupled receptor signaling pathway / negative regulation of signal transduction / GTPase activator activity / G alpha (i) signalling events / G alpha (q) signalling events / G protein-coupled receptor signaling pathway / GTPase activity / plasma membrane / cytoplasm
Similarity search - Function
Regulator of G-protein Signalling 4; domain 1 - #10 / Regulator of G-protein Signalling 4; domain 1 / RGS, subdomain 1/3 / Regulator of G-protein Signalling 4, domain 2 / Regulator of G-protein Signalling 4; domain 2 / Regulator of G protein signaling domain / RGS domain / RGS domain profile. / Regulator of G protein signalling domain / RGS, subdomain 2 ...Regulator of G-protein Signalling 4; domain 1 - #10 / Regulator of G-protein Signalling 4; domain 1 / RGS, subdomain 1/3 / Regulator of G-protein Signalling 4, domain 2 / Regulator of G-protein Signalling 4; domain 2 / Regulator of G protein signaling domain / RGS domain / RGS domain profile. / Regulator of G protein signalling domain / RGS, subdomain 2 / RGS domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Regulator of G-protein signaling 18
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, molecular dynamics
AuthorsHigman, V.A. / Leidert, M. / Bray, J. / Elkins, J. / Soundararajan, M. / Doyle, D.A. / Gileadi, C. / Phillips, C. / Schoch, G. / Yang, X. ...Higman, V.A. / Leidert, M. / Bray, J. / Elkins, J. / Soundararajan, M. / Doyle, D.A. / Gileadi, C. / Phillips, C. / Schoch, G. / Yang, X. / Brockmann, C. / Schmieder, P. / Diehl, A. / Sundstrom, M. / Arrowsmith, C. / Weigelt, J. / Edwards, A. / Oschkinat, H. / Ball, L.J. / Structural Genomics Consortium (SGC)
Citation
Journal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: Structural diversity in the RGS domain and its interaction with heterotrimeric G protein alpha-subunits.
Authors: Soundararajan, M. / Willard, F.S. / Kimple, A.J. / Turnbull, A.P. / Ball, L.J. / Schoch, G.A. / Gileadi, C. / Fedorov, O.Y. / Dowler, E.F. / Higman, V.A. / Hutsell, S.Q. / Sundstrom, M. / ...Authors: Soundararajan, M. / Willard, F.S. / Kimple, A.J. / Turnbull, A.P. / Ball, L.J. / Schoch, G.A. / Gileadi, C. / Fedorov, O.Y. / Dowler, E.F. / Higman, V.A. / Hutsell, S.Q. / Sundstrom, M. / Doyle, D.A. / Siderovski, D.P.
History
DepositionOct 11, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
SupersessionJun 20, 2012ID: 2H33
Revision 1.3Jun 20, 2012Group: Other
Revision 1.4Aug 15, 2012Group: Other
Revision 1.5Feb 5, 2020Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.6Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.7Dec 20, 2023Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.deposit_site
Revision 1.8May 8, 2024Group: Database references / Category: database_2 / Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Regulator of G-protein signaling 18


Theoretical massNumber of molelcules
Total (without water)17,7861
Polymers17,7861
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Regulator of G-protein signaling 18 / RGS18


Mass: 17786.023 Da / Num. of mol.: 1 / Fragment: RGS domain, residues 75-223
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: BL21 (DE3) strain enriched with genes that encode rare tRNAs
Gene: RGS18, RGS13 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) - Rosetta / References: UniProt: Q9NS28

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1223D HNCO
1323D CBCA(CO)NNH
1423D CBCACONNH
1523D HN(CA)CO
1623D H(CCO)NNH
1723D HBHA(CO)NNH
1823D (H)CCH-TOCSY
1923D (H)CCH-COSY
11013D 1H-15N NOESY HSQC
11123D 1H-13C NOESY HSQC
11233D 1H-13C HMQC NOESY
11332D 1H-13C HSQC
11432D TOCSY

-
Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-95% 15N] RGS18, 20 mM sodium phosphate, 50 mM sodium chloride, 10 % D2O, 1 mM [U-99% 2H] DTT, 0.02 % sodium azide90% H2O/10% D2O
21 mM [U-95% 13C; U-95% 15N] RGS18, 20 mM potassium phosphate, 50 mM sodium chloride, 10 % D2O, 1 mM [U-99% 2H] DTT, 0.02 % sodium azide90% H2O/10% D2O
31 mM [U-95% 13C; U-95% 15N] RGS18, 20 mM potassium phosphate, 50 mM sodium chloride, 100 % D2O, 1 mM [U-99% 2H] DTT, 0.02 % sodium azide100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMRGS18[U-95% 15N]1
20 mMsodium phosphate1
50 mMsodium chloride1
10 %D2O1
1 mMDTT[U-99% 2H]1
0.02 %sodium azide1
1 mMRGS18[U-95% 13C; U-95% 15N]2
20 mMpotassium phosphate2
50 mMsodium chloride2
10 %D2O2
1 mMDTT[U-99% 2H]2
0.02 %sodium azide2
1 mMRGS18[U-95% 13C; U-95% 15N]3
20 mMpotassium phosphate3
50 mMsodium chloride3
100 %D2O3
1 mMDTT[U-99% 2H]3
0.02 %sodium azide3
Sample conditionspH: 6 / Pressure: ambient / Temperature: 297 K

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DMXBrukerDMX7502
Bruker DRXBrukerDRX6003

-
Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6 and 3.1Bruker Biospincollection
XwinNMR2.6 and 3.1Bruker Biospinprocessing
CcpNmr Analysis1.0.9-10Vranken,Boucher,Stevens,Fogh,Pajon,Llinas,Ulrich,Markley,Ionides,Laueprocessing
CcpNmr Analysis1.0.9-10Vranken,Boucher,Stevens,Fogh,Pajon,Llinas,Ulrich,Markley,Ionides,Lauedata analysis
CYANA2Guntert,Mumenthaler,Wuthrichstructure solution
X-PLOR NIH2.14Schwieters,Kuszewski,Tjandra,Clorestructure solution
X-PLOR NIH2.14Schwieters,Kuszewski,Tjandra,Clorerefinement
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
Details: NOE ASSIGNMENT WITH CYANA, REFINEMENT BY SIMULATED ANNEALING IN XPLOR-NIH USING NOE RESTRAINTS AND H-BOND RESTRAINTS FROM H/D EXCHANGE DATA. WATER-REFINEMENT BY MOLECULAR DYNAMICS IN XPLOR- ...Details: NOE ASSIGNMENT WITH CYANA, REFINEMENT BY SIMULATED ANNEALING IN XPLOR-NIH USING NOE RESTRAINTS AND H-BOND RESTRAINTS FROM H/D EXCHANGE DATA. WATER-REFINEMENT BY MOLECULAR DYNAMICS IN XPLOR-NIH. THE C-TERMINAL TAIL HAS BEEN TRUNCATED PAST RESIDUE 134 BECAUSE OF FLEXIBILITY AND LACK OF STRUCTURE IN THIS REGION. THIS IS INDICATED (A) BY A LACK OF NOE RESTRAINTS PAST RESIDUE 132 AND (B) BY 15N T1, T2 AND HETERONCULEAR NOE EXPERIMENTS RESIDUE 131 ONWARDS.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: lowest energy / Conformers calculated total number: 200 / Conformers submitted total number: 20

+
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