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- PDB-2jm5: Solution Structure of the RGS domain from human RGS18 -

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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, subdomain 2 / RGS domain / RGS domain profile. / Regulator of G protein signalling domain ...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, subdomain 2 / RGS domain / RGS domain profile. / Regulator of G protein signalling domain / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Regulator of G-protein signaling 18


Theoretical massNumber of molelcules
Total (without water)17,7861
Polymers17,7861
Non-polymers00
Water0
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

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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

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Experimental details

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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

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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: 6.0 / Pressure: ambient / Temperature: 297 K

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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

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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

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