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- PDB-2cpi: Solution structure of the RNA recognition motif of CNOT4 -

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Basic information

Entry
Database: PDB / ID: 2cpi
TitleSolution structure of the RNA recognition motif of CNOT4
ComponentsCCR4-NOT transcription complex subunit 4
KeywordsGENE REGULATION / RNA recognition motif / RRM / RNP / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / Deadenylation of mRNA / CCR4-NOT complex / regulation of megakaryocyte differentiation / protein autoubiquitination / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / ubiquitin-dependent protein catabolic process / protein ubiquitination / RNA binding ...TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / Deadenylation of mRNA / CCR4-NOT complex / regulation of megakaryocyte differentiation / protein autoubiquitination / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / ubiquitin-dependent protein catabolic process / protein ubiquitination / RNA binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
CNOT4, RNA recognition motif / NOT4, modified RING finger, HC subclass (C4C4-type) / CCR4-NOT transcription complex subunit 4 / RNA recognition motif domain, eukaryote / RNA recognition motif / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / RRM (RNA recognition motif) domain / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. ...CNOT4, RNA recognition motif / NOT4, modified RING finger, HC subclass (C4C4-type) / CCR4-NOT transcription complex subunit 4 / RNA recognition motif domain, eukaryote / RNA recognition motif / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / RRM (RNA recognition motif) domain / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
CCR4-NOT transcription complex subunit 4
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / torsion angle dyanamics, simulated annealing
AuthorsNagata, T. / Muto, Y. / Inoue, M. / Kigawa, T. / Terada, T. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the RNA recognition motif of CNOT4
Authors: Nagata, T. / Muto, Y. / Inoue, M. / Kigawa, T. / Terada, T. / Shirouzu, M. / Yokoyama, S.
History
DepositionMay 19, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 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_ref_seq_dif / struct_sheet
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_ref_seq_dif.details / _struct_sheet.number_strands
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED
Remark 700SHEET DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CCR4-NOT transcription complex subunit 4


Theoretical massNumber of molelcules
Total (without water)11,7061
Polymers11,7061
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 / 100target function,structures with the lowest energy,structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein CCR4-NOT transcription complex subunit 4 / E3 ubiquitin protein ligase CNOT4 / CCR4-associated factor 4 / Potential transcriptional repressor NOT4Hp


Mass: 11706.180 Da / Num. of mol.: 1 / Fragment: RNA recognition motif
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: Cell-free protein synthesis / Gene: Cnot4 / Plasmid: p040727-12
References: UniProt: Q8BT14, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)

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Experimental details

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Experiment

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

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Sample preparation

DetailsContents: 0.75mM 13C/15N-PROTEIN; 20mM d-Tris-HCl(pH7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Brukercollection
NMRPipe20030801/20031121Delaglio, F.processing
NMRView5.0.4Johnson, B.A.data analysis
KUJIRA0.925Kobayashi, N.data analysis
CYANA2.0.17Guntert, P.structure solution
CYANA2.0.17Guntert, P.refinement
RefinementMethod: torsion angle dyanamics, simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function,structures with the lowest energy,structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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