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- PDB-2i5o: Solution Structure of the Ubiquitin-Binding Zinc Finger (UBZ) Dom... -

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Basic information

Entry
Database: PDB / ID: 2i5o
TitleSolution Structure of the Ubiquitin-Binding Zinc Finger (UBZ) Domain of the Human DNA Y-Polymerase Eta
ComponentsDNA polymerase eta
KeywordsTRANSFERASE / ZINC FINGER / DNA POLYMERASE / POL ETA / UBZ / UBIQUITIN-BINDING ZINC FINGER / TRANSLESION SYNTHESIS / UBIQUITIN-BINDING DOMAIN
Function / homology
Function and homology information


response to UV-C / DNA synthesis involved in DNA repair / error-free translesion synthesis / cellular response to UV-C / pyrimidine dimer repair / error-prone translesion synthesis / regulation of DNA repair / replication fork / Termination of translesion DNA synthesis / Translesion Synthesis by POLH ...response to UV-C / DNA synthesis involved in DNA repair / error-free translesion synthesis / cellular response to UV-C / pyrimidine dimer repair / error-prone translesion synthesis / regulation of DNA repair / replication fork / Termination of translesion DNA synthesis / Translesion Synthesis by POLH / response to radiation / HDR through Homologous Recombination (HRR) / site of double-strand break / DNA replication / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA repair / nucleoplasm / nucleus / metal ion binding / cytosol
Similarity search - Function
Ubiquitin-Binding Zinc Finger / DNA polymerase eta, ubiquitin-binding zinc finger / Zinc finger UBZ3-type profile. / DNApol eta/Rev1, HhH motif / DNA polymerase, Y-family, little finger domain / impB/mucB/samB family C-terminal domain / UmuC domain / DNA polymerase, Y-family, little finger domain superfamily / impB/mucB/samB family / UmuC domain profile. ...Ubiquitin-Binding Zinc Finger / DNA polymerase eta, ubiquitin-binding zinc finger / Zinc finger UBZ3-type profile. / DNApol eta/Rev1, HhH motif / DNA polymerase, Y-family, little finger domain / impB/mucB/samB family C-terminal domain / UmuC domain / DNA polymerase, Y-family, little finger domain superfamily / impB/mucB/samB family / UmuC domain profile. / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / Structure originally calculated by torsion angle dynamics, refined by water refinement.
AuthorsZhou, P. / Bomar, M.G.
CitationJournal: Embo Rep. / Year: 2007
Title: Structure of the ubiquitin-binding zinc finger domain of human DNA Y-polymerase eta.
Authors: Bomar, M.G. / Pai, M.T. / Tzeng, S.R. / Li, S.S. / Zhou, P.
History
DepositionAug 25, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / 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_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 600 HELIX DETERMINATION METHOD: AUTHOR PROVIDED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA polymerase eta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,4872
Polymers4,4221
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 30structures with acceptable covalent geometry
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide DNA polymerase eta / RAD30 homolog A / Xeroderma pigmentosum variant type protein


Mass: 4422.001 Da / Num. of mol.: 1 / Fragment: Ubiquitin-Binding Zinc Finger (UBZ)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLH / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)STAR / References: UniProt: Q9Y253, DNA-directed DNA polymerase
#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 15N-separated NOESY
1243D 13C-separated NOESY
132triple resonance experiments
14313C HSQC
154(H)CCH-TOCSY
162RDC experiments

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Sample preparation

Details
Solution-IDContentsSolvent system
12 mM Pol Eta UBZ; U-15N; 25 mM phosphate, 100 mM KCl, 95% H20, 5% D20, 2 mM DTT25 mM phosphate, 100 mM KCl, 95% H20, 5% D20, 2 mM DTT
22 mM Pol Eta UBZ; U-15N, 13C; 25 mM phosphate, 100 mM KCl, 95% H20, 5% D20, 2 mM DTT25 mM phosphate, 100 mM KCl, 95% H20, 5% D20, 2 mM DTT
32 mM Pol Eta UBZ; 10%-13C; 25 mM phosphate, 100 mM KCl, 95% H20, 5% D20, 2 mM DTT25 mM phosphate, 100 mM KCl, 95% H20, 5% D20, 2 mM DTT
42 mM Pol Eta UBZ; U-15N, 13C; 25 mM phosphate, 100 mM KCl, 100% D20, 2 mM DTT25 mM phosphate, 100 mM KCl, 100% D20, 2 mM DTT
Sample conditionsIonic strength: 100 mM KCl / pH: 7 / Pressure: ambient / Temperature: 298 K

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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
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guentertstructure solution
XPLOR-NIH2.9.7Schwietersrefinement
NMRPipe2.3Delaglioprocessing
XEASY/CARA1.5.1Bartelsdata analysis
RefinementMethod: Structure originally calculated by torsion angle dynamics, refined by water refinement.
Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry
Conformers calculated total number: 30 / Conformers submitted total number: 15

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