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- PDB-2ej4: Functional and structural basis of nuclear localization signal in... -

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Basic information

Entry
Database: PDB / ID: 2ej4
TitleFunctional and structural basis of nuclear localization signal in ZIC3 zinc finger domain: a role of conserved tryptophan residue in the zinc finger domain
ComponentsZinc finger protein ZIC 3
KeywordsGENE REGULATION / zf-C2H2 domain / zinc binding / 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 / Transcriptional regulation of pluripotent stem cells / limb morphogenesis / 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 / central nervous system development / skeletal 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 / metal ion binding / nucleus / 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, restrained molecular dynamics
AuthorsTomizawa, T. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Functional and structural basis of nuclear localization signal in ZIC3 zinc finger domain: a role of conserved tryptophan residue in the zinc finger domain
Authors: Hatayama, M. / Tomizawa, T. / Bouvagnet, P. / Yokoyama, S. / Mikoshiba, K. / Kigawa, T. / Aruga, J.
History
DepositionMar 14, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 9, 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)10,7633
Polymers10,6321
Non-polymers1312
Water0
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,structures with the lowest energy,target function
RepresentativeModel #1lowest energy

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Components

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


Mass: 10631.933 Da / Num. of mol.: 1 / Fragment: ZIC3_C2H2-12 domain, UNP residues 245-326
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: ZIC3 / Plasmid: P050815-02 / References: UniProt: O60481
#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 13C-separated NOESY
1213D 15N-separated NOESY

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Sample preparation

DetailsContents: 1.13mM ZIC3_C2H2-12 U-15N,13C; 20mM d-malonic acid-NaOH(pH6.0); 100mM NaCl; 0.1mM d-DTT; 0.02% NaN3; 0.05mM ZnCl2; 1mM NTA; 90% H2O,10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 6.0 / Pressure: ambient / Temperature: 296 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
KUJIRA0.932Kobayashi, N.data analysis
CYANA2.1Guntert, P.structure solution
CYANA2.1Guntert, P.refinement
RefinementMethod: torsion angle dynamics, restrained molecular dynamics
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations,structures with the lowest energy,target function
Conformers calculated total number: 100 / Conformers submitted total number: 20

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