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- PDB-2v6z: Solution Structure of Amino-Terminal Domain of Human DNA Polymera... -

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Basic information

Entry
Database: PDB / ID: 2v6z
TitleSolution Structure of Amino-Terminal Domain of Human DNA Polymerase Epsilon Subunit B
ComponentsDNA POLYMERASE EPSILON SUBUNIT 2
KeywordsTRANSFERASE / DNA REPLICATION / DNA POLYMERASE EPSILON / DPOE2 / AAA PROTEIN FAMILY
Function / homology
Function and homology information


epsilon DNA polymerase complex / DNA replication initiation / PCNA-Dependent Long Patch Base Excision Repair / Activation of the pre-replicative complex / error-prone translesion synthesis / Gap-filling DNA repair synthesis and ligation in GG-NER / Recognition of DNA damage by PCNA-containing replication complex / Termination of translesion DNA synthesis / HDR through Homologous Recombination (HRR) / Dual Incision in GG-NER ...epsilon DNA polymerase complex / DNA replication initiation / PCNA-Dependent Long Patch Base Excision Repair / Activation of the pre-replicative complex / error-prone translesion synthesis / Gap-filling DNA repair synthesis and ligation in GG-NER / Recognition of DNA damage by PCNA-containing replication complex / Termination of translesion DNA synthesis / HDR through Homologous Recombination (HRR) / Dual Incision in GG-NER / DNA-templated DNA replication / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / DNA replication / DNA-directed DNA polymerase activity / nuclear body / DNA repair / intracellular membrane-bounded organelle / DNA binding / nucleoplasm
Similarity search - Function
DNA polymerase epsilon subunit B, N-terminal / DNA polymerases epsilon N terminal / DNA polymerase epsilon, subunit B / DNA polymerase alpha/delta/epsilon, subunit B / DNA polymerase alpha/epsilon subunit B / Helicase, Ruva Protein; domain 3 - #60 / Helicase, Ruva Protein; domain 3 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA polymerase epsilon subunit 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodSOLUTION NMR / simulated annealing
AuthorsNuutinen, T. / Fredriksson, K. / Tossavainen, H. / Pospiech, H. / Pirila, P. / Permi, P. / Annila, A. / Syvaoja, J.E.
CitationJournal: Nucleic Acids Res. / Year: 2008
Title: The Solution Structure of the Amino-Terminal Domain of Human DNA Polymerase Epsilon Subunit B is Homologous to C-Domains of Aaa+ Proteins.
Authors: Nuutinen, T. / Tossavainen, H. / Fredriksson, K. / Pirila, P. / Permi, P. / Pospiech, H. / Syvaoja, J.E.
History
DepositionJul 24, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 5, 2008Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Other / Refinement description / Version format compliance
Revision 1.2Jul 24, 2013Group: Derived calculations / Other / Source and taxonomy
Revision 2.0Jan 17, 2018Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Structure summary
Category: atom_site / citation ...atom_site / citation / pdbx_nmr_spectrometer / struct
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _citation.page_last / _pdbx_nmr_spectrometer.manufacturer / _pdbx_nmr_spectrometer.model / _struct.title
Revision 2.1Jan 15, 2020Group: Data collection / Other / Category: pdbx_database_status / pdbx_nmr_software
Item: _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name
Revision 2.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
M: DNA POLYMERASE EPSILON SUBUNIT 2


Theoretical massNumber of molelcules
Total (without water)11,0881
Polymers11,0881
Non-polymers00
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 / 300LOWEST NOE RESTRAINT VIOLATION ENERGIES
RepresentativeModel #1

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Components

#1: Protein DNA POLYMERASE EPSILON SUBUNIT 2 / / DNA POLYMERASE II SUBUNIT 2 / DNA POLYMERASE EPSILON / SUBUNIT B / DPOE2


Mass: 11087.515 Da / Num. of mol.: 1 / Fragment: AMINO TERMINAL DOMAIN, RESIDUES 1-75 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PRSFDUET-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P56282, DNA-directed DNA polymerase
Compound detailsENGINEERED RESIDUE IN CHAIN M, CYS 74 TO SER
Sequence detailsMGSSHHHHHHSQDPNSSSARLQVD IS NON-BIOLOGICAL SEQUENCE.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D-15N-SEPARATED NOESY
1213D 13C-SEPARATED NOESY
NMR detailsText: NONE

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Sample preparation

Details
Solution-IDContents
10.7 MM PROTEIN
2155 MM NACL
325 MM TRIS-HCL
425 MM IMIDAZOLE
51.25 MM EDTA
693% H2O, 7% D2O
Sample conditionspH: 6.62 / Pressure: 1.0 atm / Temperature: 298.0 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
Amber8D.A.CASE,T.A.DARDEN,T.E CHEATHAM III,C.L. SIMMERLING,J.WANG,R.E.DUKE,R.LUO,K.M.MERZ, B.WANG,D.A.PEARLMAN,M.CROWLEY,S.BROZELL, V.TSUI,H.GOHLKE,J.MONGAN,V.HORNAK,G.CUI, P.BEROZA,C.SCHAFMEISTER,J.W.CALDWELL,W.S.ROSSrefinement
CYANAstructure solution
Amber8structure solution
PROCHECK / PROCHECK-NMRNMRstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: THE STRUCTURES ARE BASED ON A TOTAL OF 1488 DISTANCE RESTRAINTS.
NMR ensembleConformer selection criteria: LOWEST NOE RESTRAINT VIOLATION ENERGIES
Conformers calculated total number: 300 / Conformers submitted total number: 20

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