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

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Basic information

Entry
Database: PDB / ID: 2mki
TitleSolution structure of tandem RRM domains of cytoplasmic polyadenylation element binding protein 4 (CPEB4) in complex with RNA
Components
  • Cytoplasmic polyadenylation element-binding protein 4
  • RNA (5'-R(*CP*UP*UP*UP*A)-3')
KeywordsTRANSLATION REGULATOR/RNA / CPEB4 / Cytoplasmic polyadenylation / RNA recognition motif (RRM) / Protein-RNA Interaction / Translational regulation / TRANSLATION REGULATOR-RNA complex
Function / homology
Function and homology information


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 / response to ischemia / mRNA 3'-UTR binding / cellular response to amino acid stimulus / ribosome binding ...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 / response to ischemia / mRNA 3'-UTR binding / cellular response to amino acid stimulus / ribosome binding / growth cone / dendritic spine / negative regulation of neuron apoptotic process / neuron projection / postsynaptic density / synapse / dendrite / perinuclear region of cytoplasm / endoplasmic reticulum / RNA binding / metal ion binding / nucleus / 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
RNA / Cytoplasmic polyadenylation element-binding protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model3
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 1.1May 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytoplasmic polyadenylation element-binding protein 4
B: RNA (5'-R(*CP*UP*UP*UP*A)-3')


Theoretical massNumber of molelcules
Total (without water)24,3342
Polymers24,3342
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 53-255
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
#2: RNA chain RNA (5'-R(*CP*UP*UP*UP*A)-3')


Mass: 1507.928 Da / Num. of mol.: 1 / Source method: obtained synthetically
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
1152D 1H-15N HSQC
1222D 1H-13C HSQC
1322D 1H-13C HSQC aliphatic
1422D 1H-13C HSQC aromatic
1552D 1H-1H TOCSY
1642D 1H-1H NOESY
1733D trHNCA
1833D trHN(CO)CA
1933D trCBCA(CO)NH
11033D trHNCACB
11133D trHNCO
11233D trHCACO
11313D (H)CCH-TOCSY
11453D 1H-15N NOESY
11533D 1H-13C NOESY aliphatic
11633D 1H-13C NOESY aromatic
11733D (H)CCH-TOCSY
11852D 1H-15N TROSY
11912D 13C F1-filtered F2-filtered NOESY
12012D 1H-1H F1-13C-filtered F2-13C-edited NOESY
12113D 13C F1-edited, F3-filtered NOESY HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
150 mM sodium phosphate-1, 100 mM sodium chloride-2, 1 mM DTT-3, 0.6 mM [U-100% 13C; U-100% 15N] CPEB4RRM12-4, 0.6 mM 5'-CUUUA-3'-5, 90% H2O/10% D2O90% H2O/10% D2O
20.4-0.6 mM [U-100% 13C; U-100% 15N] CPEB4RRM12-6, 0.4-06 mM RNA (5'-CUUUA)-3')-7, 100 mM sodium chloride-8, 1 mM DTT-9, 50 mM sodium phosphate-10, 100% D2O100% D2O
30.4-0.6 mM [U-100% 13C; U-100% 15N; U-80% 2H] CPEB4RRM12-11, 0.4-0.6 mM 5'-CUUUA-3'-12, 100 mM sodium chloride-13, 1 mM DTT-14, 50 mM sodium phosphate-15, 90% H2O/10% D2O90% H2O/10% D2O
40.4-0.6 mM [U-100% 15N] CPEB4RRM12-16, 0.4-0.6 mM 5'-CUUUA-3'-17, 100 mM sodium chloride-18, 1 mM DTT-19, 50 mM potassium phosphate-20, 100% D2O100% D2O
50.4-0.6 mM [U-100% 15N] CPEB4RRM12-21, 0.4-0.6 mM 5'-CUUUA-3'-22, 100 mM sodium chloride-23, 1 mM DTT-24, 50 mM potassium phosphate-25, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
50 mMsodium phosphate-11
100 mMsodium chloride-21
1 mMDTT-31
0.6 mMCPEB4RRM12-4[U-100% 13C; U-100% 15N]1
0.6 mM5'-CUUUA-3'-51
mMCPEB4RRM12-6[U-100% 13C; U-100% 15N]0.4-0.62
mMRNA (5'-CUUUA)-3')-70.4-062
100 mMsodium chloride-82
1 mMDTT-92
50 mMsodium phosphate-102
mMCPEB4RRM12-11[U-100% 13C; U-100% 15N; U-80% 2H]0.4-0.63
mM5'-CUUUA-3'-120.4-0.63
100 mMsodium chloride-133
1 mMDTT-143
50 mMsodium phosphate-153
mMCPEB4RRM12-16[U-100% 15N]0.4-0.64
mM5'-CUUUA-3'-170.4-0.64
100 mMsodium chloride-184
1 mMDTT-194
50 mMpotassium phosphate-204
mMCPEB4RRM12-21[U-100% 15N]0.4-0.65
mM5'-CUUUA-3'-220.4-0.65
100 mMsodium chloride-235
1 mMDTT-245
50 mMpotassium phosphate-255
Sample conditionsIonic strength: 0.15 / pH: 7 / 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: 3

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