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- PDB-2m13: The ZZ domain of cytoplasmic polyadenylation element binding prot... -

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Basic information

Entry
Database: PDB / ID: 2m13
TitleThe ZZ domain of cytoplasmic polyadenylation element binding protein 1 (CPEB1)
ComponentsCytoplasmic polyadenylation element-binding protein 1
KeywordsMETAL BINDING PROTEIN / Zinc-binding protein / ZZ motif
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 ...: / 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 / nucleus / metal ion binding / cytoplasm / cytosol
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 / molecular dynamics, torsion angle dynamics
Model detailslowest energy, model1
AuthorsLee, B.M. / Merkel, D.J. / Wells, S.B. / Hilburn, B.C. / Elazzouzi, F. / Perez-Alvarado, G.C.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: The C-Terminal Region of Cytoplasmic Polyadenylation Element Binding Protein Is a ZZ Domain with Potential for Protein-Protein Interactions.
Authors: Merkel, D.J. / Wells, S.B. / Hilburn, B.C. / Elazzouzi, F. / Perez-Alvarado, G.C. / Lee, B.M.
History
DepositionNov 14, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 3, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Database references
Revision 1.2May 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_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_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_ref_seq_dif.details / _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)7,9003
Polymers7,7691
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)20 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 7768.841 Da / Num. of mol.: 1 / Fragment: ZZ domain of CPEB1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CPEB, CPEB1 / Plasmid: pMal / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 / References: UniProt: Q9BZB8
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-15N HSQC
1312D 1H-1H NOESY
1422D 1H-1H NOESY
1512D 1H-13C ct-HSQC aliphatic
1622D 1H-13C ct-HSQC aliphatic
1712D 1H-13C HMQC aromatic
1822D 1H-13C HMQC aromatic
1922D 1H-15N HMQC 2JNH
11012D (HB)CB(CGCD)HD
11113D HNCO
11223D HNCO
11313D HNCA
11423D HNCA
11513D HN(CA)CB
11613D CBCA(CO)NH
11723D CBCA(CO)NH
11813D (H)CCH-COSY
11923D (H)CCH-COSY
12013D 1H-15N/13C NOESY
12123D 1H-15N/13C NOESY
12213D (H)CCH-TOCSY
12313D C(CO)NH

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Sample preparation

Details
Solution-IDContentsSolvent system
10.3 mM [U-100% 13C; U-100% 15N] CPEB1-ZZ G-P-504, 20 mM TRIS, 200 mM sodium chloride, 1 mM DTT, 90% H2O/10% D2O90% H2O/10% D2O
20.3 mM [U-100% 13C; U-100% 15N] CPEB1-ZZ T498S, 50 mM potassium phosphate, 200 mM potassium chloride, 5 mM DTT, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.3 mMCPEB1-ZZ G-P-504-566-1[U-100% 13C; U-100% 15N]1
20 mMTRIS-21
200 mMsodium chloride-31
1 mMDTT-41
0.3 mMCPEB1-ZZ T498S-566-5[U-100% 13C; U-100% 15N]2
50 mMpotassium phosphate-62
200 mMpotassium chloride-72
5 mMDTT-82
Sample conditionsIonic strength: 200 / pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UnityPlusVarianUNITYPLUS5001
Varian UnityPlusVarianUNITYPLUS6002

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Processing

NMR software
NameVersionDeveloperClassification
Amber10Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
CYANA1.0.5Guntert, Mumenthaler and Wuthrichrefinement
TALOS_plusShen, Delaglio, Cornilescu and Baxdata analysis
MOLMOLKoradi, Billeter and Wuthrichdata analysis
ProcheckNMRLaskowski and MacArthurdata analysis
NMRView8.0.3Johnson, One Moon Scientificdata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: molecular dynamics, torsion angle dynamics / Software ordinal: 1 / Details: implicit solvent ff03
NMR constraintsNOE constraints total: 352 / NOE intraresidue total count: 32 / NOE long range total count: 176 / NOE medium range total count: 121 / NOE sequential total count: 112 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 25 / Protein psi angle constraints total count: 26
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: 0 ° / Maximum upper distance constraint violation: 0.14 Å

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