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- PDB-2jnu: Solution structure of the RGS domain of human RGS14 -

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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 / regulation of G protein-coupled receptor signaling pathway / GTPase activating protein binding / GDP-dissociation inhibitor activity / nucleocytoplasmic transport / positive regulation of neurogenesis / spindle organization / negative regulation of G protein-coupled receptor signaling pathway / platelet-derived growth factor receptor signaling pathway ...zygote asymmetric cell division / negative regulation of synaptic plasticity / regulation of G protein-coupled receptor signaling pathway / GTPase activating protein binding / GDP-dissociation inhibitor activity / nucleocytoplasmic transport / positive regulation of neurogenesis / spindle organization / negative regulation of G protein-coupled receptor signaling pathway / platelet-derived growth factor receptor signaling pathway / G-protein alpha-subunit binding / long-term memory / negative regulation of MAP kinase activity / GTPase activator activity / learning / chromosome segregation / long-term synaptic potentiation / visual learning / PML body / negative regulation of ERK1 and ERK2 cascade / spindle pole / spindle / signaling receptor complex adaptor activity / mitotic cell cycle / G alpha (i) signalling events / microtubule binding / response to oxidative stress / microtubule / dendritic spine / postsynaptic density / nuclear body / G protein-coupled receptor signaling pathway / cell division / GTPase activity / centrosome / glutamatergic synapse / dendrite / protein kinase binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
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 ...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 domain / RGS domain profile. / Regulator of G protein signalling domain / RGS, subdomain 2 / 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, 2007Deposition site: RCSB / Processing 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
Revision 1.4Jun 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 1.5Dec 20, 2023Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.deposit_site
Revision 1.6May 8, 2024Group: Database references / Category: database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Regulator of G-protein signaling 14


Theoretical massNumber of molelcules
Total (without water)17,7181
Polymers17,7181
Non-polymers00
Water00
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

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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

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Experimental details

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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.

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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)
16ambient 297 K
26.2ambient 297 K

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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

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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

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