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- PDB-2mke: Solution structure of CPEB1 ZZ domain in the free state -

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Basic information

Entry
Database: PDB / ID: 2mke
TitleSolution structure of CPEB1 ZZ domain in the free state
ComponentsCytoplasmic polyadenylation element-binding protein 1
KeywordsTRANSLATION REGULATOR / CPEB1 / CPEB4 / RRM / Cytoplasmic Polyadenylation Element / Translation regulation
Function / homology
Function and homology information


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 ...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 / neuron projection / postsynaptic density / ribonucleoprotein complex / synapse / dendrite / nucleoplasm / metal ion binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
Cytoplasmic polyadenylation element-binding protein, ZZ domain / 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 / 30s Ribosomal Protein S18 ...Cytoplasmic polyadenylation element-binding protein, ZZ domain / 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 / 30s Ribosomal Protein S18 / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Few Secondary Structures / Irregular / Nucleotide-binding alpha-beta plait domain superfamily
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 6, 2014Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jul 23, 2014Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_conn_angle / struct_conn / struct_site
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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytoplasmic polyadenylation element-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,5183
Polymers7,3871
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)26 / 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: 7387.414 Da / Num. of mol.: 1 / Fragment: UNP residues 426-486
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: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
Sequence detailsTHE RESIDUE NUMBERS ARE BASED ON 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
1613D CBCA(CO)NH
1713D HNCO
1813D HNCA
1913D HN(CA)CB
11013D (H)CCH-TOCSY
11113D 1H-15N NOESY
11213D 1H-13C NOESY aliphatic
11313D 1H-13C NOESY aromatic
11412D 1H-1H NOESY

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Sample preparation

DetailsContents: 0.4-0.6 mM [U-100% 13C; U-100% 15N] CPEB1ZZ-1, 0.4-0.6 mM [U-100% 15N] CPEB1ZZ-2, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMCPEB1ZZ-1[U-100% 13C; U-100% 15N]0.4-0.61
mMCPEB1ZZ-2[U-100% 15N]0.4-0.61
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: 26 / Representative conformer: 2

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