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

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Basic information

Entry
Database: PDB / ID: 2mkj
TitleSolution structure of tandem RRM domains of cytoplasmic polyadenylation element binding protein 4 (CPEB4) in free state
ComponentsCytoplasmic polyadenylation element-binding protein 4
KeywordsTRANSLATION REGULATOR / CPEB4 / RNA recognition motif (RRM) / Cytoplasmic polyadenylation / Translational regulation
Function / homology
Function and homology information


messenger ribonucleoprotein complex / cellular response to decreased oxygen levels / translation factor activity, RNA binding / negative regulation of cytoplasmic translation / cellular response to glucose starvation / ionotropic glutamate receptor signaling pathway / mRNA regulatory element binding translation repressor activity / mRNA 3'-UTR binding / response to ischemia / cellular response to amino acid stimulus ...messenger ribonucleoprotein complex / cellular response to decreased oxygen levels / translation factor activity, RNA binding / negative regulation of cytoplasmic translation / cellular response to glucose starvation / ionotropic glutamate receptor signaling pathway / mRNA regulatory element binding translation repressor activity / mRNA 3'-UTR binding / response to ischemia / cellular response to amino acid stimulus / ribosome binding / growth cone / negative regulation of neuron apoptotic process / dendritic spine / postsynaptic density / neuron projection / synapse / dendrite / perinuclear region of cytoplasm / endoplasmic reticulum / RNA binding / nucleus / metal ion binding / 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 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model4
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 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
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 4


Theoretical massNumber of molelcules
Total (without water)22,8261
Polymers22,8261
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 / 30structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Cytoplasmic polyadenylation element-binding protein 4 / CPE-BP4 / CPE-binding protein 4 / hCPEB-4


Mass: 22825.979 Da / Num. of mol.: 1 / Fragment: UNP residues 53-254
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CPEB4, KIAA1673 / Production host: Escherichia coli (E. coli) / References: UniProt: Q17RY0
Sequence detailsTHIS PROTEIN SEQUENCE IS ISOFORM 3 OF CPEB4_HUMAN.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1132D 1H-15N HSQC
1232D TROSY
1312D 1H-13C HSQC
1412D 1H-13C HSQC aliphatic
1512D 1H-13C HSQC aromatic
1642D 1H-1H TOCSY
1742D 1H-1H NOESY
1823D CBCA(CO)NH
1923D trHNCACB
11023D trHNCA
11123D trHN(CO)CA
11233D trHNCO
11323D trHCACO
11413D (H)CCH-TOCSY
11513D (H)CCH-TOCSY
11623D 1H-15N NOESY
11713D 1H-13C NOESY aliphatic
11813D 1H-13C NOESY aromatic

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Sample preparation

Details
Solution-IDContentsSolvent system
10.4-0.6 mM [U-100% 13C; U-100% 15N] CPEB4RRM12-1, 100 mM sodium chloride-2, 50 mM sodium phosphate-3, 1 mM DTT-4, 90% H2O/10% D2O90% H2O/10% D2O
20.4-0.6 mM [U-100% 13C; U-100% 15N; U-80% 2H] CPEB4RRM12-5, 100 mM sodium chloride-6, 50 mM sodium phosphate-7, 1 mM DTT-8, 90% H2O/10% D2O90% H2O/10% D2O
30.4-0.6 mM [U-100% 15N] CPEB4RRM12-9, 100 mM sodium chloride-10, 50 mM sodium phosphate-11, 1 mM DTT-12, 90% H2O/10% D2O90% H2O/10% D2O
40.4-0.6 mM [U-100% 15N] CPEB4RRM12-13, 100 mM sodium chloride-14, 50 mM sodium phosphate-15, 1 mM DTT-16, 100% D2O100% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMCPEB4RRM12-1[U-100% 13C; U-100% 15N]0.4-0.61
100 mMsodium chloride-21
50 mMsodium phosphate-31
1 mMDTT-41
mMCPEB4RRM12-5[U-100% 13C; U-100% 15N; U-80% 2H]0.4-0.62
100 mMsodium chloride-62
50 mMsodium phosphate-72
1 mMDTT-82
mMCPEB4RRM12-9[U-100% 15N]0.4-0.63
100 mMsodium chloride-103
50 mMsodium phosphate-113
1 mMDTT-123
mMCPEB4RRM12-13[U-100% 15N]0.4-0.64
100 mMsodium chloride-144
50 mMsodium phosphate-154
1 mMDTT-164
Sample conditionsIonic strength: 0.15 / pH: 7.0 / 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 software
NameDeveloperClassification
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
SparkyGoddardchemical shift assignment
TopSpinBruker Biospinprocessing
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: 4

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