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- PDB-2yue: Solution structure of the NEUZ (NHR) domain in Neuralized from Dr... -

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Basic information

Entry
Database: PDB / ID: 2yue
TitleSolution structure of the NEUZ (NHR) domain in Neuralized from Drosophila melanogaster
ComponentsProtein neuralized
KeywordsRNA BINDING PROTEIN / structure genomics / NEUZ(NHR) domain / Neuralized / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


regulation of photoreceptor cell differentiation / regulation of compound eye photoreceptor development / negative regulation of lamellocyte differentiation / sensory organ precursor cell fate determination / sensory organ development / neuroblast fate determination / compound eye development / asymmetric cell division / ventral cord development / imaginal disc-derived wing morphogenesis ...regulation of photoreceptor cell differentiation / regulation of compound eye photoreceptor development / negative regulation of lamellocyte differentiation / sensory organ precursor cell fate determination / sensory organ development / neuroblast fate determination / compound eye development / asymmetric cell division / ventral cord development / imaginal disc-derived wing morphogenesis / phosphatidylinositol phosphate binding / germ-line stem cell population maintenance / peripheral nervous system development / positive regulation of Notch signaling pathway / mesoderm development / positive regulation of endocytosis / long-term memory / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / protein localization / nervous system development / perinuclear region of cytoplasm / DNA binding / zinc ion binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Neuralized homology repeat (NHR) domain / Neuralized / Neuralized / Neuralized homology repeat (NHR) domain profile. / NEUZ / SPRY domain / Zinc finger, C3HC4 type (RING finger) / B30.2/SPRY domain superfamily / Ring finger / Zinc finger RING-type profile. ...Neuralized homology repeat (NHR) domain / Neuralized / Neuralized / Neuralized homology repeat (NHR) domain profile. / NEUZ / SPRY domain / Zinc finger, C3HC4 type (RING finger) / B30.2/SPRY domain superfamily / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesDrosophila melanogaster (fruit fly)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsHe, F. / Muto, Y. / Inoue, M. / Kigawa, T. / Shirouzu, M. / Tarada, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Structural and functional characterization of the NHR1 domain of the Drosophila neuralized E3 ligase in the notch signaling pathway.
Authors: He, F. / Saito, K. / Kobayashi, N. / Harada, T. / Watanabe, S. / Kigawa, T. / Guntert, P. / Ohara, O. / Tanaka, A. / Unzai, S. / Muto, Y. / Yokoyama, S.
History
DepositionApr 6, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 9, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 23, 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_ref_seq_dif
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_ref_seq_dif.details
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 650HELIX Determination method: Author determined
Remark 700SHEET Determination method: Author determined

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein neuralized


Theoretical massNumber of molelcules
Total (without water)18,9401
Polymers18,9401
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 / 100structures with the least restraint violations, target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Protein neuralized


Mass: 18940.266 Da / Num. of mol.: 1 / Fragment: NEUZ(NHR) domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Description: cell-free protein synthesis / Plasmid: P061002-04 / References: UniProt: P29503

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY

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Sample preparation

DetailsContents: 1.0mM 13C, 15N-labeled protein; 20mM d-Tris-HCl(pH 7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Brukercollection
NMRPipe20030801Delaglio, F.processing
NMRView5.0.4Johnson, B.A.data analysis
KUJIRA0.982Kobayashi, N.data analysis
CYANA2.1Guntert, P.structure solution
CYANA2.1Guntert, 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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