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- PDB-1k18: Minimized Average NMR Structure of the Zinc Finger Domain of Huma... -

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Basic information

Entry
Database: PDB / ID: 1k18
TitleMinimized Average NMR Structure of the Zinc Finger Domain of Human DNA Polymerase-alpha
ComponentsDNA POLYMERASE ALPHA CATALYTIC SUBUNIT
KeywordsTRANSFERASE / zinc finger protein / DNA binding domain / polymerase-alpha
Function / homology
Function and homology information


DNA replication initiation / Telomere C-strand synthesis initiation / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / regulation of type I interferon production / Polymerase switching / alpha DNA polymerase:primase complex / Processive synthesis on the lagging strand / Removal of the Flap Intermediate / Polymerase switching on the C-strand of the telomere / DNA replication, synthesis of primer ...DNA replication initiation / Telomere C-strand synthesis initiation / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / regulation of type I interferon production / Polymerase switching / alpha DNA polymerase:primase complex / Processive synthesis on the lagging strand / Removal of the Flap Intermediate / Polymerase switching on the C-strand of the telomere / DNA replication, synthesis of primer / lagging strand elongation / mitotic DNA replication initiation / DNA strand elongation involved in DNA replication / DNA synthesis involved in DNA repair / leading strand elongation / G1/S-Specific Transcription / DNA replication origin binding / DNA replication initiation / Activation of the pre-replicative complex / Defective pyroptosis / double-strand break repair via nonhomologous end joining / nuclear matrix / nuclear envelope / single-stranded DNA binding / DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA repair / nucleotide binding / chromatin binding / chromatin / nucleolus / protein kinase binding / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
DNA polymerase alpha catalytic subunit, N-terminal domain / DNA polymerase alpha, zinc finger domain superfamily / DNA Polymerase alpha zinc finger / DNA polymerase alpha subunit p180 N terminal / Zinc finger, DNA-directed DNA polymerase, family B, alpha / DNA polymerase alpha catalytic subunit, catalytic domain / DNA polymerase family B, thumb domain / DNA-directed DNA polymerase, family B, multifunctional domain / DNA polymerase family B signature. / DNA-directed DNA polymerase, family B, conserved site ...DNA polymerase alpha catalytic subunit, N-terminal domain / DNA polymerase alpha, zinc finger domain superfamily / DNA Polymerase alpha zinc finger / DNA polymerase alpha subunit p180 N terminal / Zinc finger, DNA-directed DNA polymerase, family B, alpha / DNA polymerase alpha catalytic subunit, catalytic domain / DNA polymerase family B, thumb domain / DNA-directed DNA polymerase, family B, multifunctional domain / DNA polymerase family B signature. / DNA-directed DNA polymerase, family B, conserved site / DNA polymerase family B / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain / DNA polymerase, palm domain superfamily / DNA polymerase type-B family / DNA-directed DNA polymerase, family B / Ribonuclease H superfamily / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
DNA polymerase alpha catalytic subunit
Similarity search - Component
MethodSOLUTION NMR / simulated annealing, restrained molecular mechanics
Model type detailsminimized average
AuthorsEvanics, F. / Maurmann, L. / Yang, W.W. / Bose, R.N.
Citation
Journal: Biochim.Biophys.Acta / Year: 2003
Title: Nuclear magnetic resonance structures of the zinc finger domain of human DNA polymerase-alpha.
Authors: Evanics, F. / Maurmann, L. / Yang, W.W. / Bose, R.N.
#1: Journal: J.CHEM.SOC.,CHEM.COMMUN. / Year: 2003
Title: Unwinding of DNA polymerases by the antitumor drug, cis-diamminedichloroplatinum(II)
Authors: Volckova, E. / Evanics, F. / Yang, W.W. / Bose, R.N.
History
DepositionSep 24, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 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
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
Revision 1.4May 22, 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: DNA POLYMERASE ALPHA CATALYTIC SUBUNIT


Theoretical massNumber of molelcules
Total (without water)3,5361
Polymers3,5361
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)1 / -
Representativeminimized average structure

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Components

#1: Protein/peptide DNA POLYMERASE ALPHA CATALYTIC SUBUNIT


Mass: 3536.204 Da / Num. of mol.: 1 / Fragment: zinc finger domain (residues 1347-1377) / Source method: obtained synthetically / Details: The sequence occurs naturally in humans. / References: UniProt: P09884, DNA-directed DNA polymerase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121DQF-COSY
131TOCSY
NMR detailsText: This structure was determined using standard 2D homonuclear experiments. The NOESY mixing time was 200 ms.

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Sample preparation

DetailsContents: 3mM Zinc Finger Peptide; 3.6 mM Zn(II)nitrate / Solvent system: 90% H2O/10% D2O
Sample conditionspH: 6.8 / Pressure: ambient / Temperature: 296 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE8001
Varian UNITYVarianUNITY5002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3BRUKERprocessing
CORMA5.2Borgias; Thomas; Liu; Kumar; Tonelliiterative matrix relaxation
MARDIGRAS3.2Borgias; Thomas; Liu; Kumar; Tonelliiterative matrix relaxation
DGII97MSIstructure solution
Discover97MSIrefinement
RefinementMethod: simulated annealing, restrained molecular mechanics / Software ordinal: 1
Details: 190 NOE derived distance restraints and 4 dihedral angle restraints were used for the calculations.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformers submitted total number: 1

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