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- PDB-1wjv: Solution structure of the N-terminal zinc finger domain of mouse ... -

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Basic information

Entry
Database: PDB / ID: 1wjv
TitleSolution structure of the N-terminal zinc finger domain of mouse cell growth regulating nucleolar protein LYAR
ComponentsCell growth regulating nucleolar protein LYAR
KeywordsDNA BINDING PROTEIN / Cell growth regulating nucleolar protein LYAR / DNA-binding protein / C2H2 type zinc-finger / structural genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


DNA-binding transcription factor binding => GO:0140297 / transcription regulator inhibitor activity / positive regulation of transcription by RNA polymerase I / photoreceptor outer segment / erythrocyte development / positive regulation of phagocytosis / negative regulation of innate immune response / rRNA processing / innate immune response / nucleolus ...DNA-binding transcription factor binding => GO:0140297 / transcription regulator inhibitor activity / positive regulation of transcription by RNA polymerase I / photoreceptor outer segment / erythrocyte development / positive regulation of phagocytosis / negative regulation of innate immune response / rRNA processing / innate immune response / nucleolus / negative regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / identical protein binding / nucleus / metal ion binding / cytoplasm
Similarity search - Function
Dna Ligase; domain 1 - #490 / Zinc finger, C2H2, LYAR-type / Cell growth-regulating nucleolar protein / LYAR-type C2HC zinc finger / Zinc finger C2HC LYAR-type profile. / Zinc finger C2H2 superfamily / Dna Ligase; domain 1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Cell growth-regulating nucleolar protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsYoneyama, M. / Tochio, N. / Koshiba, S. / Inoue, M. / Kigawa, T. / Muto, Y. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the N-terminal zinc finger domain of mouse cell growth regulating nucleolar protein LYAR
Authors: Yoneyama, M. / Tochio, N. / Koshiba, S. / Inoue, M. / Kigawa, T. / Muto, Y. / Yokoyama, S.
History
DepositionMay 29, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 29, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / 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_nmr_spectrometer.model / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cell growth regulating nucleolar protein LYAR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,5413
Polymers8,4101
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 / 100structures with the least restraint violations, target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Cell growth regulating nucleolar protein LYAR


Mass: 8410.414 Da / Num. of mol.: 1 / Fragment: Zinc finger DNA binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: Cell-free protein synthesis / Gene: RIKEN cDNA 1700026C17 / Plasmid: P030421-25 / References: UniProt: Q08288
#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
1113D 15N-separated NOESY
1223D 13C-separated NOESY

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Sample preparation

DetailsContents: 1mM zinc finger DNA binding domain U-15N, 13C; 20mM d-Tris-HCl; 200mM NaCl; 1mM d-DTT; 0.02% NaN3; 100uM ZnCl2; 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 220mM / pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
NMRPipe20020425Delagio, F.processing
NMRView5.0.4Jhonson, B.A.data analysis
KUJIRA0.896Kobayashi, N.data analysis
CYANA2.0.17Guentert, P.structure solution
CYANA2.0.17Guentert, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations, target function
Conformers calculated total number: 100 / Conformers submitted total number: 20

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