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- PDB-2rok: Solution structure of the cap-binding domain of PARN complexed wi... -

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Basic information

Entry
Database: PDB / ID: 2rok
TitleSolution structure of the cap-binding domain of PARN complexed with the cap analog
Componentspoly(A)-specific ribonuclease
KeywordsRNA BINDING PROTEIN / RRM / RBD / CAP / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


KSRP (KHSRP) binds and destabilizes mRNA / Deadenylation of mRNA / cation binding / box H/ACA sno(s)RNA 3'-end processing / poly(A)-specific ribonuclease / poly(A)-specific ribonuclease activity / miRNA catabolic process / poly(A)-dependent snoRNA 3'-end processing / nuclear-transcribed mRNA poly(A) tail shortening / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay ...KSRP (KHSRP) binds and destabilizes mRNA / Deadenylation of mRNA / cation binding / box H/ACA sno(s)RNA 3'-end processing / poly(A)-specific ribonuclease / poly(A)-specific ribonuclease activity / miRNA catabolic process / poly(A)-dependent snoRNA 3'-end processing / nuclear-transcribed mRNA poly(A) tail shortening / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / postsynapse / glutamatergic synapse / nucleolus / RNA binding / nucleus / metal ion binding / cytoplasm
Similarity search - Function
Poly(A)-specific ribonuclease, RNA-binding / PARN, R3H domain / RNA binding domain / Ribonuclease CAF1 / R3H domain / CAF1 family ribonuclease / R3H domain / R3H domain superfamily / R3H domain profile. / RNA-binding domain superfamily ...Poly(A)-specific ribonuclease, RNA-binding / PARN, R3H domain / RNA binding domain / Ribonuclease CAF1 / R3H domain / CAF1 family ribonuclease / R3H domain / R3H domain superfamily / R3H domain profile. / RNA-binding domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
7N-METHYL-8-HYDROGUANOSINE-5'-MONOPHOSPHATE / GUANOSINE-5'-DIPHOSPHATE / Poly(A)-specific ribonuclease PARN / Poly(A)-specific ribonuclease PARN
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
AuthorsNagata, T. / Suzuki, S. / Endo, R. / Shirouzu, M. / Terada, T. / Inoue, M. / Kigawa, T. / Guntert, P. / Hayashizaki, Y. / Muto, Y. ...Nagata, T. / Suzuki, S. / Endo, R. / Shirouzu, M. / Terada, T. / Inoue, M. / Kigawa, T. / Guntert, P. / Hayashizaki, Y. / Muto, Y. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Nucleic Acids Res. / Year: 2008
Title: The RRM domain of poly(A)-specific ribonuclease has a noncanonical binding site for mRNA cap analog recognition.
Authors: Nagata, T. / Suzuki, S. / Endo, R. / Shirouzu, M. / Terada, T. / Inoue, M. / Kigawa, T. / Kobayashi, N. / Guntert, P. / Tanaka, A. / Hayashizaki, Y. / Muto, Y. / Yokoyama, S.
History
DepositionMar 28, 2008Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Feb 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: poly(A)-specific ribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8363
Polymers11,0131
Non-polymers8222
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 / 40structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein poly(A)-specific ribonuclease / Polyadenylate-specific ribonuclease


Mass: 11013.168 Da / Num. of mol.: 1 / Fragment: cap-binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Parn
References: UniProt: Q3TUQ8, UniProt: Q8VDG3*PLUS, poly(A)-specific ribonuclease
#2: Chemical ChemComp-7MG / 7N-METHYL-8-HYDROGUANOSINE-5'-MONOPHOSPHATE


Type: RNA linking / Mass: 379.263 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O8P
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-13C NOESY
1213D 1H-15N NOESY

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Sample preparation

DetailsContents: 0.5 mM [U-100% 13C; U-100% 15N] PARN, 2.5 mM M7GpppG, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMPARN[U-100% 13C; U-100% 15N]1
2.5 mMM7GpppG1
Sample conditionsIonic strength: 120 / pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe20060702Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRView5.0.4Johnson, One Moon Scientificdata analysis
NMRView5.0.4Johnson, One Moon Scientificpeak picking
XwinNMR3.5Bruker Biospincollection
KUJIRA0.9825Naohiro Kobayashidata analysis
KUJIRA0.9825Naohiro Kobayashichemical shift assignment
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
Amber9Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, Kollmrefinement
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 40 / Conformers submitted total number: 20

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