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- PDB-2ju4: NMR structure of the gamma subunit of cGMP phosphodiesterase -

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Basic information

Entry
Database: PDB / ID: 2ju4
TitleNMR structure of the gamma subunit of cGMP phosphodiesterase
ComponentsRetinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit gamma
KeywordsHYDROLASE / Intrinsic Disordered Protein / Paramagnetic Relaxation Enhancement / cGMP / Sensory transduction / Vision / Structural Genomics / PSI-2 / Protein Structure Initiative / Center for Eukaryotic Structural Genomics / CESG
Function / homology
Function and homology information


3',5'-cyclic-GMP phosphodiesterase / Inactivation, recovery and regulation of the phototransduction cascade / positive regulation of G protein-coupled receptor signaling pathway / Activation of the phototransduction cascade / ion binding / Ca2+ pathway / response to stimulus / positive regulation of epidermal growth factor receptor signaling pathway / photoreceptor outer segment membrane / 3',5'-cyclic-GMP phosphodiesterase activity ...3',5'-cyclic-GMP phosphodiesterase / Inactivation, recovery and regulation of the phototransduction cascade / positive regulation of G protein-coupled receptor signaling pathway / Activation of the phototransduction cascade / ion binding / Ca2+ pathway / response to stimulus / positive regulation of epidermal growth factor receptor signaling pathway / photoreceptor outer segment membrane / 3',5'-cyclic-GMP phosphodiesterase activity / cGMP binding / visual perception / photoreceptor disc membrane / positive regulation of MAPK cascade / molecular adaptor activity / zinc ion binding
Similarity search - Function
Intrinsically disordered gamma-subunit of cGMP phosphodiesterase / Retinal cGMP phosphodiesterase, gamma subunit / Retinal cGMP phosphodiesterase, gamma subunit / Retinal cGMP phosphodiesterase, gamma subunit superfamily / Retinal cGMP phosphodiesterase, gamma subunit / Few Secondary Structures / Irregular
Similarity search - Domain/homology
Chem-RCY / Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit gamma
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodSOLUTION NMR / molecular dynamics, simulated annealing
AuthorsSong, J. / Guo, L.W. / Ruoho, A.E. / Markley, J.L. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2008
Title: Intrinsically disordered gamma-subunit of cGMP phosphodiesterase encodes functionally relevant transient secondary and tertiary structure.
Authors: Song, J. / Guo, L.W. / Muradov, H. / Artemyev, N.O. / Ruoho, A.E. / Markley, J.L.
History
DepositionAug 14, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 16, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 15, 2012Group: Structure summary
Revision 1.3Feb 22, 2012Group: Non-polymer description
Revision 1.4Feb 19, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_conn / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,86511
Polymers9,4721
Non-polymers2,39310
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)100 / 200structures with the lowest energy
RepresentativeModel #1fewest violations

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Components

#1: Protein Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit gamma / GMP-PDE gamma


Mass: 9472.058 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Tissue: Retina / Gene: PDE6G, PDEG / Plasmid: pTXBI / Production host: Escherichia coli (E. coli)
References: UniProt: P04972, 3',5'-cyclic-nucleotide phosphodiesterase
#2: Chemical
ChemComp-RCY / (3'R)-1'-oxyl-2',2',5',5'-tetramethyl-1,3'-bipyrrolidine-2,5-dione / 3-Maleimido-PROXYL (bound form)


Mass: 239.291 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C12H19N2O3

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1242D 1H-1H TOCSY
1343D CBCA(CO)NH
1443D HN(CA)CB
1542D 1H-1H TOCSY
1643D HBHA(CO)NH
1743D H(CCO)NH
1843D C(CO)NH
1943D HNCO
11043D HNHA
11122D 1H-15N HSQC
11232D 1H-15N HSQC
NMR detailsText: This protein is intrinsically disordered. Because the structures are largely disordered in solution, they contain several different conformational population. Therefore all the structures can not be superimposed.

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Sample preparation

Details
Solution-IDContentsSolvent system
10.05 mM [U-100% 15N] PDEgamma, 90% H2O/10% D2O90% H2O/10% D2O
20.05 mM [U-15N] PROXYL-PDEgamma, 90% H2O/10% D2O90% H2O/10% D2O
30.05 mM [U-100% 15N] PROXYL-PDEgamma, 5 mM Ascorbic Acid, 93% H2O/7% D2O93% H2O/7% D2O
40.09 mM [U-100% 13C; U-100% 15N] PDEgamma, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.05 mMPDEgamma[U-100% 15N]1
0.05 mMPROXYL-PDEgamma[U-15N]2
0.05 mMPROXYL-PDEgamma[U-100% 15N]3
5 mMAscorbic Acid3
0.09 mMPDEgamma[U-100% 13C; U-100% 15N]4
Sample conditionsIonic strength: 0 / pH: 4 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX6001
Bruker DMXBrukerDMX7502
Varian INOVAVarianINOVA6003

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.4Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
VNMRVariancollection
Sparky2.112Goddardprocessing
XPLOR-NIH2.11.2Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: molecular dynamics, simulated annealing / Software ordinal: 1
Details: There are 10272 close contacts in this entry. The deposited structures were calculated using the combined distance restraints derived from ten single PDEgamma mutants (in each mutant a ...Details: There are 10272 close contacts in this entry. The deposited structures were calculated using the combined distance restraints derived from ten single PDEgamma mutants (in each mutant a native residue was replaced by the 3-maleimido-PROXYL-cysteine residue). As a result, the deposited structures contain 10 mutated residues which do not coexist in the process of NMR structure determination. To avoid the artificial steric hinderance between individual spin groups, the Van der Waals contacts involving the 2,2,5,5-tetramethyl-1-pyrrolidinyloxy group (but not the maleimide group) are turned off in the structure calculation.
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 100

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