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- PDB-2mkk: Structural model of tandem RRM domains of cytoplasmic polyadenyla... -

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Basic information

Entry
Database: PDB / ID: 2mkk
TitleStructural model of tandem RRM domains of cytoplasmic polyadenylation element binding protein 1 (CPEB1) in complex with RNA
Components
  • Cytoplasmic polyadenylation element-binding protein 1
  • RNA (5'-R(*UP*UP*UP*UP*A)-3')
KeywordsTRANSLATION REGULATOR/RNA / CPEB1 / RNA recognition motif (RRM) / Cytoplasmic polyadenylation / Protein-RNA Interaction / Translation regulation / TRANSLATION REGULATOR-RNA complex
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 / P-body / cellular response to amino acid stimulus / 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 / P-body / cellular response to amino acid stimulus / mRNA processing / cellular response to insulin stimulus / ribosome binding / cellular response to hypoxia / postsynaptic density / neuron projection / dendrite / synapse / 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
RNA / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytoplasmic polyadenylation element-binding protein 1
B: RNA (5'-R(*UP*UP*UP*UP*A)-3')


Theoretical massNumber of molelcules
Total (without water)25,4392
Polymers25,4392
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)10 / 20structures 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: 23930.580 Da / Num. of mol.: 1 / Fragment: UNP residues 219-430
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
#2: RNA chain RNA (5'-R(*UP*UP*UP*UP*A)-3')


Mass: 1508.912 Da / Num. of mol.: 1 / Source method: obtained synthetically
Sequence detailsTHIS PROTEIN 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
1142D 1H-15N HSQC
1242D TROSY
1322D 1H-13C HSQC
1422D 1H-13C HSQC aliphatic
1522D 1H-13C HSQC aromatic
1652D 1H-1H TOCSY
1752D 1H-1H NOESY
1813D trHNCA
1913D trHN(CO)CA
11013D trCBCA(CO)NH
11113D trHNCACB
11213D trHNCACO
11313D trHNCO
11423D (H)CCH-TOCSY
11523D (H)CCH-TOCSY
11643D 1H-15N NOESY
11713D 1H-13C NOESY aliphatic
11813D 1H-13C NOESY aromatic
11962D 13C-F1-filtered F2-filtered NOESY
12062D 1H-1H F1-13C-filtered F2-13C-edited NOESY
12163D 13C-F1-edited F3-filtered NOESY HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.4-0.6 mM [U-100% 13C; U-100% 15N; U-80% 2H] CPEB1RRM12-1, 0.4-0.6 mM 5'-UUUUA-3'-2, 100 mM sodium chloride-3, 50 mM sodium phosphate-4, 1 mM DTT-5, 1 mM magnesium sulfate-6, 90% H2O/10% D2O90% H2O/10% D2O
20.4-0.6 mM [U-100% 13C; U-100% 15N] CPEB1RRM12-7, 0.4-0.6 mM 5'-UUUUA-3'-8, 100 mM sodium chloride-9, 50 mM sodium phosphate-10, 1 mM DTT-11, 1 mM magnesium sulfate-12, 90% H2O/10% D2O90% H2O/10% D2O
30.4-0.6 mM [U-100% 13C; U-100% 15N] CPEB1RRM12-13, 0.4-0.6 mM 5'-UUUUA-3'-14, 100 mM sodium chloride-15, 50 mM sodium phosphate-16, 1 mM DTT-17, 1 mM magnesium sulfate-18, 100% D2O100% D2O
40.4-0.6 mM [U-100% 15N] CPEB1RRM12-19, 0.4-0.6 mM 5'-UUUUA-3'-20, 100 mM sodium chloride-21, 50 mM sodium phosphate-22, 1 mM DTT-23, 1 mM magnesium sulfate-24, 90% H2O/10% D2O90% H2O/10% D2O
50.4-0.6 mM [U-100% 15N] CPEB1RRM12-25, 0.4-0.6 mM 5'-UUUUA-3'-26, 100 mM sodium chloride-27, 50 mM sodium phosphate-28, 1 mM DTT-29, 1 mM magnesium sulfate-30, 100% D2O100% D2O
60.4-0.6 mM [U-100% 15N] CPEB1RRM12-31, 0.4-0.6 mM 5'-CUUUA-3'-32, 100 mM sodium chloride-33, 50 mM sodium phosphate-34, 1 mM DTT-35, 1 mM magnesium sulfate-36, 100% D2O100% D2O
70.4-0.6 mM [U-100% 13C; U-100% 15N] CPEB1RRM12-37, 0.4-0.6 mM 5'-CUUUA-3'-38, 100 mM sodium chloride-39, 50 mM sodium phosphate-40, 1 mM DTT-41, 1 mM magnesium sulfate-42, 100% D2O100% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMCPEB1RRM12-1[U-100% 13C; U-100% 15N; U-80% 2H]0.4-0.61
mM5'-UUUUA-3'-20.4-0.61
100 mMsodium chloride-31
50 mMsodium phosphate-41
1 mMDTT-51
1 mMmagnesium sulfate-61
mMCPEB1RRM12-7[U-100% 13C; U-100% 15N]0.4-0.62
mM5'-UUUUA-3'-80.4-0.62
100 mMsodium chloride-92
50 mMsodium phosphate-102
1 mMDTT-112
1 mMmagnesium sulfate-122
mMCPEB1RRM12-13[U-100% 13C; U-100% 15N]0.4-0.63
mM5'-UUUUA-3'-140.4-0.63
100 mMsodium chloride-153
50 mMsodium phosphate-163
1 mMDTT-173
1 mMmagnesium sulfate-183
mMCPEB1RRM12-19[U-100% 15N]0.4-0.64
mM5'-UUUUA-3'-200.4-0.64
100 mMsodium chloride-214
50 mMsodium phosphate-224
1 mMDTT-234
1 mMmagnesium sulfate-244
mMCPEB1RRM12-25[U-100% 15N]0.4-0.65
mM5'-UUUUA-3'-260.4-0.65
100 mMsodium chloride-275
50 mMsodium phosphate-285
1 mMDTT-295
1 mMmagnesium sulfate-305
mMCPEB1RRM12-31[U-100% 15N]0.4-0.66
mM5'-CUUUA-3'-320.4-0.66
100 mMsodium chloride-336
50 mMsodium phosphate-346
1 mMDTT-356
1 mMmagnesium sulfate-366
mMCPEB1RRM12-37[U-100% 13C; U-100% 15N]0.4-0.67
mM5'-CUUUA-3'-380.4-0.67
100 mMsodium chloride-397
50 mMsodium phosphate-407
1 mMDTT-417
1 mMmagnesium sulfate-427
Sample conditionsIonic strength: 0.15 / pH: 6.5 / Pressure: ambient atm / Temperature: 313 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
TOPSPINBruker Biospinprocessing
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
SPARKYGoddardchemical shift assignment
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: 20 / Conformers submitted total number: 10 / Representative conformer: 2

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