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- PDB-1zr9: Solution Structure of a Human C2H2-type Zinc Finger Protein -

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Basic information

Entry
Database: PDB / ID: 1zr9
TitleSolution Structure of a Human C2H2-type Zinc Finger Protein
ComponentsZinc finger protein 593
KeywordsTRANSCRIPTION / zinc finger / DNA binding / Structural Genomics / PSI / Protein Structure Initiative / Center for Eukaryotic Structural Genomics / CESG
Function / homology
Function and homology information


negative regulation of RNA polymerase II regulatory region sequence-specific DNA binding / preribosome binding / ribosome biogenesis / nucleolus / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / cytoplasm
Similarity search - Function
Zinc-finger double-stranded RNA-binding / Zinc finger, double-stranded RNA binding / Classic Zinc Finger / Matrin/U1-C-like, C2H2-type zinc finger / U1-like zinc finger / Double Stranded RNA Binding Domain / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type ...Zinc-finger double-stranded RNA-binding / Zinc finger, double-stranded RNA binding / Classic Zinc Finger / Matrin/U1-C-like, C2H2-type zinc finger / U1-like zinc finger / Double Stranded RNA Binding Domain / 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 593
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / Automated methods were used for backbone chemical shift assignment, iterative NOE refinement. Final structures were obtained by molecular dynamics in explicit solvent.
AuthorsLytle, B.L. / Peterson, F.C. / Volkman, B.F. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: Protein Sci. / Year: 2008
Title: The solution structure of ZNF593 from Homo sapiens reveals a zinc finger in a predominantly unstructured protein.
Authors: Hayes, P.L. / Lytle, B.L. / Volkman, B.F. / Peterson, F.C.
History
DepositionMay 19, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2005Provider: repository / Type: Initial release
Revision 1.1Feb 1, 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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Zinc finger protein 593
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2552
Polymers14,1901
Non-polymers651
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 / 100target function
RepresentativeModel #1closest to the average

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Components

#1: Protein Zinc finger protein 593 / / Zinc finger protein T86 / zinc finger protein LOC51042


Mass: 14189.889 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: WHEAT GERM CELL-FREE, IN VITRO EXPRESSION / Gene: ZNF593 / Plasmid: pEU(N)HIS6 / Production host: CELL-FREE SYNTHESIS (others) / References: UniProt: O00488
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / 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
1313D 13C-separated NOESY (AROMATIC)
NMR detailsText: All triple-resonance and NOESY spectra were acquired using a cyrogenic probe

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Sample preparation

DetailsContents: 0.6 mM ZNF593 U-15N,13C, 10 mM Bis Tris, 100 mM NaCl, 2 mM DTT, 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 100 mM / pH: 6.0 / 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: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Bruker Biospincollection
NMRPipe2004F. Delaglioprocessing
SPSCAN1.1.0R.W. Glaserdata analysis
XEASY1.3C. Bartelsdata analysis
GARANT2.1C. Bartelsdata analysis
CYANA1.0.6T. Herrmann, P. Guentert, K. Wuethrichstructure solution
XPLOR-NIH2.0.6G. Marius Clorerefinement
RefinementMethod: Automated methods were used for backbone chemical shift assignment, iterative NOE refinement. Final structures were obtained by molecular dynamics in explicit solvent.
Software ordinal: 1
Details: Residues 1-27 and 95-116 of the construct were disordered and were excluded from the model. After initial calculations without zinc, the zinc atom was constrained in a tetrahedral geometry ...Details: Residues 1-27 and 95-116 of the construct were disordered and were excluded from the model. After initial calculations without zinc, the zinc atom was constrained in a tetrahedral geometry using distance restraints to each coordinating CYS SG and HIS NE2 of 2.3 A and 2.0 A, respectively.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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