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- PDB-2mkh: Solution structure of tandem RRM domains of cytoplasmic polyadeny... -

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Basic information

Entry
Database: PDB / ID: 2mkh
TitleSolution structure of tandem RRM domains of cytoplasmic polyadenylation element binding protein 1 (CPEB1) in free state
ComponentsCytoplasmic polyadenylation element-binding protein 1
KeywordsTRANSLATION REGULATOR / CPEB1 / RNA recognition motif (RRM) / Cytoplasmic polyadenylation / Translational regulation
Function / homology
Function and homology information


messenger ribonucleoprotein complex / regulation of mRNA 3'-end processing / translation factor activity, RNA binding / mRNA 3'-UTR AU-rich region binding / negative regulation of cytoplasmic translation / mRNA regulatory element binding translation repressor activity / mRNA 3'-UTR binding / cellular response to amino acid stimulus / P-body / mRNA processing ...messenger ribonucleoprotein complex / regulation of mRNA 3'-end processing / translation factor activity, RNA binding / mRNA 3'-UTR AU-rich region binding / negative regulation of cytoplasmic translation / mRNA regulatory element binding translation repressor activity / mRNA 3'-UTR binding / cellular response to amino acid stimulus / P-body / mRNA processing / cellular response to insulin stimulus / ribosome binding / cellular response to hypoxia / postsynaptic density / neuron projection / synapse / dendrite / nucleoplasm / membrane / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Cytoplasmic polyadenylation element-binding protein 1, N-terminal / CPEB-1, RNA recognition motif 1 / Cytoplasmic polyadenylation element-binding protein 1 N-terminus / 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 / Eukaryotic RNA Recognition Motif (RRM) profile. ...Cytoplasmic polyadenylation element-binding protein 1, N-terminal / CPEB-1, RNA recognition motif 1 / Cytoplasmic polyadenylation element-binding protein 1 N-terminus / 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 / 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 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model2
AuthorsAfroz, T. / Skrisovska, L. / Belloc, E. / Boixet, J.G. / Mendez, R. / Allain, F.H.-T.
CitationJournal: Genes Dev. / Year: 2014
Title: A fly trap mechanism provides sequence-specific RNA recognition by CPEB proteins
Authors: Afroz, T. / Skrisovska, L. / Belloc, E. / Guillen-Boixet, J. / Mendez, R. / Allain, F.H.-T.
History
DepositionFeb 7, 2014Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jul 23, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2016Group: Structure summary
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytoplasmic polyadenylation element-binding protein 1


Theoretical massNumber of molelcules
Total (without water)24,3751
Polymers24,3751
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 / 30structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Cytoplasmic polyadenylation element-binding protein 1 / CPE-BP1 / CPE-binding protein 1 / h-CEBP / hCPEB-1


Mass: 24375.020 Da / Num. of mol.: 1 / Fragment: UNP residues 219-434
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CPEB1, CPEB / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BZB8
Sequence detailsTHIS SEQUENCE IS ISOFORM 4 OF CPEB1_HUMAN.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1312D 1H-13C HSQC aliphatic
1412D 1H-13C HSQC aromatic
1512D 1H-1H TOCSY
1612D 1H-1H NOESY
1713D HNCO
1813D CBCA(CO)NH
1913D HN(CA)CB
11013D (H)CCH-TOCSY
11113D 1H-15N NOESY
11213D 1H-13C NOESY aliphatic
11313D 1H-13C NOESY aromatic
11413D HNCA
11513D HN(CO)CA

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Sample preparation

DetailsContents: 100 mM sodium chloride-1, 1 mM DTT-2, 1 mM magnesium sulphate-3, 50 mM sodium phosphate-4, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
100 mMsodium chloride-11
1 mMDTT-21
1 mMmagnesium sulphate-31
50 mMsodium phosphate-41
Sample conditionsIonic strength: 0.15 / pH: 6.5 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE9001
Bruker AvanceBrukerAVANCE7002
Bruker AvanceBrukerAVANCE6003
Bruker AvanceBrukerAVANCE5004

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Processing

NMR softwareName: Amber
Developer: Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman
Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 30 / Conformers submitted total number: 20 / Representative conformer: 2

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