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- PDB-1n5g: NMR Structures of the Zinc Finger Domain of Human DNA Polymerase-alpha -

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Basic information

Entry
Database: PDB / ID: 1n5g
TitleNMR Structures of the Zinc Finger Domain of Human DNA Polymerase-alpha
Components38-mer of DNA 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 / alpha DNA polymerase:primase complex / Polymerase switching / regulation of type I interferon production / Processive synthesis on the lagging strand / Removal of the Flap Intermediate / Polymerase switching on the C-strand of the telomere / lagging strand elongation ...DNA replication initiation / Telomere C-strand synthesis initiation / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / alpha DNA polymerase:primase complex / Polymerase switching / regulation of type I interferon production / Processive synthesis on the lagging strand / Removal of the Flap Intermediate / Polymerase switching on the C-strand of the telomere / lagging strand elongation / DNA replication, synthesis of primer / mitotic DNA replication initiation / DNA strand elongation involved in DNA replication / DNA synthesis involved in DNA repair / G1/S-Specific Transcription / leading strand elongation / DNA replication origin binding / Activation of the pre-replicative complex / DNA replication initiation / Defective pyroptosis / nuclear matrix / double-strand break repair via nonhomologous end joining / 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 polymerase family B signature. / DNA-directed DNA polymerase, family B, conserved site / DNA polymerase family B ...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 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-directed DNA polymerase, family B, multifunctional 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, constrained molecular dynamics simulations
AuthorsEvanics, F. / Maurmann, L. / Yang, W.W. / Bose, R.N.
CitationJournal: 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.
History
DepositionNov 5, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 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_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
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: 38-mer of DNA polymerase alpha catalytic subunit


Theoretical massNumber of molelcules
Total (without water)4,4041
Polymers4,4041
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)29 / 100structures with acceptable covalent geometry
Representative

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Components

#1: Protein/peptide 38-mer of DNA polymerase alpha catalytic subunit


Mass: 4404.190 Da / Num. of mol.: 1 / Fragment: zinc finger domain (residues 1345-1382) / Source method: obtained synthetically
Details: THE PROTEIN WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THE PROTEIN IS NATURALLY FOUND IN HOMO SAPIENS.
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
1212D TOCSY
131DQF-COSY
NMR detailsText: The structure was determined using standard 2D homonuclear techniques. The NOESY mixing times were varied 75 - 500 ms.

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Sample preparation

DetailsContents: 3mM peptide, 3.6mM Zn(II)nitrate / Solvent system: 90% H2O/10% D2O
Sample conditionspH: 6.2 / 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 spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1 Rev. CVariancollection
NMRPipeDelaglio, F., Vuister, G.W., Zhu, G., Pfeifer, J.processing
NMRView5.0.3Johnson, B.A.data analysis
Discover97MSIrefinement
RefinementMethod: simulated annealing, constrained molecular dynamics simulations
Software ordinal: 1
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry
Conformers calculated total number: 100 / Conformers submitted total number: 29

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