[English] 日本語
Yorodumi
- PDB-2jnu: Solution structure of the RGS domain of human RGS14 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2jnu
TitleSolution structure of the RGS domain of human RGS14
ComponentsRegulator of G-protein signaling 14
KeywordsSIGNALING PROTEIN / Regulator of G-protein signalling domain / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


zygote asymmetric cell division / negative regulation of synaptic plasticity / negative regulation of G protein-coupled receptor signaling pathway / regulation of G protein-coupled receptor signaling pathway / regulation of DNA-templated transcription in response to stress / GDP-dissociation inhibitor activity / positive regulation of neurogenesis / GTPase activating protein binding / nucleocytoplasmic transport / spindle organization ...zygote asymmetric cell division / negative regulation of synaptic plasticity / negative regulation of G protein-coupled receptor signaling pathway / regulation of G protein-coupled receptor signaling pathway / regulation of DNA-templated transcription in response to stress / GDP-dissociation inhibitor activity / positive regulation of neurogenesis / GTPase activating protein binding / nucleocytoplasmic transport / spindle organization / platelet-derived growth factor receptor signaling pathway / G-protein alpha-subunit binding / long-term memory / GTPase activator activity / long-term synaptic potentiation / learning / negative regulation of MAP kinase activity / visual learning / signaling receptor complex adaptor activity / chromosome segregation / PML body / negative regulation of ERK1 and ERK2 cascade / spindle / spindle pole / G alpha (i) signalling events / positive regulation of GTPase activity / mitotic cell cycle / microtubule binding / response to oxidative stress / microtubule / dendritic spine / nuclear body / postsynaptic density / G protein-coupled receptor signaling pathway / intracellular signal transduction / cell division / centrosome / GTPase activity / dendrite / glutamatergic synapse / protein kinase binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Regulator of G-protein signalling 14 / RGS14, RGS domain / Regulator of G-protein Signalling 4; domain 1 - #10 / GoLoco motif / GoLoco motif / GoLoco/GPR motif profile. / LGN motif, putative GEFs specific for G-alpha GTPases / 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 14 / RGS14, RGS domain / Regulator of G-protein Signalling 4; domain 1 - #10 / GoLoco motif / GoLoco motif / GoLoco/GPR motif profile. / LGN motif, putative GEFs specific for G-alpha GTPases / 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, subdomain 2 / RGS domain / RGS domain profile. / Regulator of G protein signalling domain / RGS domain superfamily / Raf-like Ras-binding domain / Raf-like Ras-binding / Ras-binding domain (RBD) profile. / Raf-like Ras-binding domain / Ubiquitin-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Regulator of G-protein signaling 14
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsDowler, E.F. / Diehl, A. / Bray, J. / Elkins, J. / Soundararajan, M. / Doyle, D.A. / Gileadi, C. / Phillips, C. / Schoch, G.A. / Yang, X. ...Dowler, E.F. / Diehl, A. / Bray, J. / Elkins, J. / Soundararajan, M. / Doyle, D.A. / Gileadi, C. / Phillips, C. / Schoch, G.A. / Yang, X. / Brockmann, C. / Leidert, M. / Rehbein, K. / Schmieder, P. / Kuhne, R. / Higman, V.A. / Sundstrom, M. / Arrowsmith, C. / Weigelt, J. / Edwards, A. / Oschkinat, H. / Ball, L.J. / Structural Genomics Consortium (SGC)
CitationJournal: 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
DepositionFeb 2, 2007Processing site: RCSB
Revision 1.0Feb 27, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 5, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_sample_details / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_sample_details.contents ..._pdbx_database_status.status_code_cs / _pdbx_nmr_sample_details.contents / _pdbx_nmr_software.name / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Regulator of G-protein signaling 14


Theoretical massNumber of molelcules
Total (without water)17,7181
Polymers17,7181
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Regulator of G-protein signaling 14 / RGS14


Mass: 17717.902 Da / Num. of mol.: 1 / Fragment: RGS domain, sequence database residues 56-207
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: RGS14 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta BL21(DE3) / References: UniProt: O43566

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D 1H-15N NOESY
1323D CBCANH
1423D CBCA(CO)NH
2533D HNCO
2633D HN(CA)CO
1743D (H)CCH-COSY
1843D 1H-13C HMQC NOESY
1942D 1H-1H NOESY
11042D DQF-COSY
11143D (H)CCH-TOCSY
NMR detailsText: Only the structured RGS domain region, from residue 1-136 of our construct, is shown here. The unstructured C-terminal tail, from residue 137-154, has been truncated for ease of viewing. The ...Text: Only the structured RGS domain region, from residue 1-136 of our construct, is shown here. The unstructured C-terminal tail, from residue 137-154, has been truncated for ease of viewing. The flexibility of the C-terminal residues is supported by (a) 15NT1, 15NT2 and heteronuclear NOE data (b) lack of significant NOEs in this region.

-
Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-95% 15N] RGS14, 20 mM sodium phosphate, 50 mM sodium chloride, 10 % D2O, 1 mM [U-99% 2H] DTT, 90% H2O/10% D2O90% H2O/10% D2O
21.7 mM [U-95% 13C; U-95% 15N] RGS14, 20 mM sodium phosphate, 50 mM sodium chloride, 1 mM [U-99% 2H] DTT, 10 % D2O, 90% H2O/10% D2O90% H2O/10% D2O
31.4 mM [U-95% 13C; U-95% 15N] RGS14, 20 mM sodium phosphate, 50 mM sodium chloride, 1 mM [U-99% 2H] DTT, 10 % D2O, 90% H2O/10% D2O90% H2O/10% D2O
41.1 mM [U-95% 13C; U-95% 15N] RGS14, 20 mM sodium phosphate, 50 mM sodium chloride, 1 mM [U-99% 2H] DTT, 100 % [U-100% 2H] D2O, 0.02 % sodium azide, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMRGS14[U-95% 15N]1
20 mMsodium phosphate1
50 mMsodium chloride1
10 %D2O1
1 mMDTT[U-99% 2H]1
1.7 mMRGS14[U-95% 13C; U-95% 15N]2
20 mMsodium phosphate2
50 mMsodium chloride2
1 mMDTT[U-99% 2H]2
10 %D2O2
1.4 mMRGS14[U-95% 13C; U-95% 15N]3
20 mMsodium phosphate3
50 mMsodium chloride3
1 mMDTT[U-99% 2H]3
10 %D2O3
1.1 mMRGS14[U-95% 13C; U-95% 15N]4
20 mMsodium phosphate4
50 mMsodium chloride4
1 mMDTT[U-99% 2H]4
100 %D2O[U-100% 2H]4
0.02 %sodium azide4
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
16 ambient 297 K
26.2 ambient 297 K

-
NMR measurement

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

-
Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6 and 3.1Bruker Biospincollection
XwinNMR2.6 and 3.1Bruker Biospinprocessing
Sparky3.1Goddardpeak picking
Sparky3.1Goddardchemical shift assignment
Sparky3.1Goddarddata analysis
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
X-PLOR NIH2.14Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIH2.14Schwieters, Kuszewski, Tjandra and Clorerefinement
CNSSOLVE1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The final ensemble was refined in explicit water to improve Z-scores, side-chain packing and the appearance of the Ramachandran plot.
NMR constraintsNOE constraints total: 1958 / NOE intraresidue total count: 0 / NOE long range total count: 690 / NOE medium range total count: 584 / NOE sequential total count: 623 / Hydrogen bond constraints total count: 67
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0.3 Å / Maximum torsion angle constraint violation: 5 ° / Maximum upper distance constraint violation: 0.3 Å

+
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