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- PDB-2rpc: Solution structure of the tandem zf-C2H2 domains from the human z... -

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Basic information

Entry
Database: PDB / ID: 2rpc
TitleSolution structure of the tandem zf-C2H2 domains from the human zinc finger protein ZIC 3
ComponentsZinc finger protein ZIC 3
KeywordsTRANSCRIPTION / zf-C2H2 / Zinc finger protein of the cerebellum 3 / ZIC3 / Disease mutation / DNA-binding / Metal-binding / Nucleus / Polymorphism / Transcription regulation / Zinc / Zinc-finger / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


central nervous system segmentation / determination of left/right asymmetry in nervous system / determination of pancreatic left/right asymmetry / determination of digestive tract left/right asymmetry / determination of liver left/right asymmetry / atrial cardiac muscle tissue development / neural plate development / primitive streak formation / POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation / left/right axis specification ...central nervous system segmentation / determination of left/right asymmetry in nervous system / determination of pancreatic left/right asymmetry / determination of digestive tract left/right asymmetry / determination of liver left/right asymmetry / atrial cardiac muscle tissue development / neural plate development / primitive streak formation / POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation / left/right axis specification / germ-line stem cell population maintenance / limb morphogenesis / Transcriptional regulation of pluripotent stem cells / cranial skeletal system development / paraxial mesoderm development / olfactory bulb development / embryonic pattern specification / axial mesoderm development / outer ear morphogenesis / determination of left/right symmetry / smoothened signaling pathway / heart looping / face development / skeletal system development / central nervous system development / stem cell differentiation / hippocampus development / lung development / mRNA transcription by RNA polymerase II / neuron differentiation / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / transcription coactivator activity / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / metal ion binding / cytoplasm
Similarity search - Function
ZIC protein, zinc finger domain / Zic proteins zinc finger domain / Classic Zinc Finger / Zinc finger, C2H2 type / Double Stranded RNA Binding Domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type ...ZIC protein, zinc finger domain / Zic proteins zinc finger domain / Classic Zinc Finger / Zinc finger, C2H2 type / Double Stranded RNA Binding Domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Zinc finger protein ZIC 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsTomizawa, T. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Hum.Mol.Genet. / Year: 2008
Title: Functional and structural basis of the nuclear localization signal in the ZIC3 zinc finger domain
Authors: Hatayama, M. / Tomizawa, T. / Sakai-Kato, K. / Bouvagnet, P. / Kose, S. / Imamoto, N. / Yokoyama, S. / Utsunomiya-Tate, N. / Mikoshiba, K. / Kigawa, T. / Aruga, J.
History
DepositionMay 14, 2008Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Mar 31, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 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 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3May 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: Zinc finger protein ZIC 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8675
Polymers17,6051
Non-polymers2624
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 / 100target function
RepresentativeModel #1fewest violations

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Components

#1: Protein Zinc finger protein ZIC 3 / Zinc finger protein of the cerebellum 3


Mass: 17604.984 Da / Num. of mol.: 1 / Fragment: C2H2 domains, UNP residues 245-386
Source method: isolated from a genetically manipulated source
Details: E. coli - cell free / Source: (gene. exp.) Homo sapiens (human) / Gene: ZIC3 / Production host: cell free system (unknown) / References: UniProt: O60481
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / 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 1H-15N NOESY
1213D 1H-13C NOESY

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Sample preparation

DetailsContents: 0.57mM [U-13C; U-15N] zinc finger protein ZIC 3; 20mM [U-2H] TRIS; 100mM sodium chloride; 1mM [U-2H] DTT; 0.02 % sodium azide; 0.05mM ZnCl2; 1mM IDA; 10% [U-2H] D2O; 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.57 mMzinc finger protein ZIC 3[U-13C; U-15N]1
20 mMTRIS[U-2H]1
100 mMsodium chloride1
1 mMDTT[U-2H]1
0.02 %sodium azide1
0.05 mMZnCl21
1 mMIDA1
10 %D2O[U-2H]1
Sample conditionsIonic strength: 120 / pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 900 MHz

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificdata analysis
KUJIRAKobayashi, Ndata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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