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- PDB-2rug: Refined solution structure of the first RNA recognition motif dom... -

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Basic information

Entry
Database: PDB / ID: 2rug
TitleRefined solution structure of the first RNA recognition motif domain in CPEB3
ComponentsCytoplasmic polyadenylation element-binding protein 3
KeywordsRNA BINDING PROTEIN / RRM domain / RBD / Structural Genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


negative regulation of cytoplasmic translational elongation / : / CCR4-NOT complex / regulation of dendritic spine development / apical dendrite / 3'-UTR-mediated mRNA destabilization / translation factor activity, RNA binding / mRNA 3'-UTR AU-rich region binding / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / positive regulation of dendritic spine development ...negative regulation of cytoplasmic translational elongation / : / CCR4-NOT complex / regulation of dendritic spine development / apical dendrite / 3'-UTR-mediated mRNA destabilization / translation factor activity, RNA binding / mRNA 3'-UTR AU-rich region binding / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / positive regulation of dendritic spine development / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / negative regulation of cytoplasmic translation / long-term memory / mRNA regulatory element binding translation repressor activity / positive regulation of translation / mRNA 3'-UTR binding / cellular response to amino acid stimulus / regulation of synaptic plasticity / RNA stem-loop binding / ribosome binding / midbody / postsynaptic density / negative regulation of translation / neuron projection / dendrite / synapse / negative regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Cytoplasmic polyadenylation element-binding protein, ZZ domain / Cytoplasmic polyadenylation element-binding protein / CEBP, ZZ domain superfamily / Cytoplasmic polyadenylation element-binding protein ZZ domain / RNA recognition motif / RRM (RNA recognition motif) domain / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily ...Cytoplasmic polyadenylation element-binding protein, ZZ domain / Cytoplasmic polyadenylation element-binding protein / CEBP, ZZ domain superfamily / Cytoplasmic polyadenylation element-binding protein ZZ domain / RNA recognition motif / RRM (RNA recognition motif) domain / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Cytoplasmic polyadenylation element-binding protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailsfewest violations, model1
AuthorsTsuda, K. / Kuwasako, K. / Nagata, T. / Takahashi, M. / Kigawa, T. / Kobayashi, N. / Guntert, P. / Shirouzu, M. / Yokoyama, S. / Muto, Y. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Proteins / Year: 2014
Title: Novel RNA recognition motif domain in the cytoplasmic polyadenylation element binding protein 3.
Authors: Tsuda, K. / Kuwasako, K. / Nagata, T. / Takahashi, M. / Kigawa, T. / Kobayashi, N. / Guntert, P. / Shirouzu, M. / Yokoyama, S. / Muto, Y.
History
DepositionApr 15, 2014Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Sep 17, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Data collection / Database references
Category: citation / database_2 ...citation / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.2Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / 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: Cytoplasmic polyadenylation element-binding protein 3


Theoretical massNumber of molelcules
Total (without water)12,4291
Polymers12,4291
Non-polymers00
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 / 200structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein Cytoplasmic polyadenylation element-binding protein 3 / CPE-BP3 / CPE-binding protein 3 / hCPEB-3


Mass: 12428.833 Da / Num. of mol.: 1 / Fragment: RNA recognition motif, UNP RESIDUES 440-540
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Escherichia coli / Gene: CPEB3, KIAA0940 / Production host: Cell-free synthesis (others) / References: UniProt: Q8NE35

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1213D 1H-13C NOESY
1312D 1H-15N HSQC
1412D 1H-13C HSQC

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Sample preparation

DetailsContents: 1.06 mM [U-100% 13C; U-100% 15N] entity-1, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 1.06 mM / Component: entity-1 / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 120 / pH: 7 / 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
XwinNMR3.5Bruker Biospincollection
NMRPipe20030801Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRView5.0.4Johnson, One Moon Scientificdata analysis
KUJIRA0.9843Kobayashi, Ndata analysis
CYANA2.0.17Guntert, Mumenthaler and Wuthrichstructure solution
Amber9Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmanrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 1

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