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- PDB-2n1g: Structure of C-terminal domain of human polymerase Rev1 in comple... -

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Basic information

Entry
Database: PDB / ID: 2n1g
TitleStructure of C-terminal domain of human polymerase Rev1 in complex with PolD3 RIR-motif
Components
  • DNA polymerase delta subunit 3
  • DNA repair protein REV1
KeywordsTRANSFERASE / Rev1 / PolD3
Function / homology
Function and homology information


delta DNA polymerase complex / DNA synthesis involved in UV-damage excision repair / deoxycytidyl transferase activity / zeta DNA polymerase complex / nucleotide-excision repair, DNA gap filling / Polymerase switching / Telomere C-strand (Lagging Strand) Synthesis / Processive synthesis on the lagging strand / Removal of the Flap Intermediate / Processive synthesis on the C-strand of the telomere ...delta DNA polymerase complex / DNA synthesis involved in UV-damage excision repair / deoxycytidyl transferase activity / zeta DNA polymerase complex / nucleotide-excision repair, DNA gap filling / Polymerase switching / Telomere C-strand (Lagging Strand) Synthesis / Processive synthesis on the lagging strand / Removal of the Flap Intermediate / Processive synthesis on the C-strand of the telomere / Polymerase switching on the C-strand of the telomere / Removal of the Flap Intermediate from the C-strand / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / error-free translesion synthesis / DNA biosynthetic process / DNA synthesis involved in DNA repair / DNA strand elongation involved in DNA replication / PCNA-Dependent Long Patch Base Excision Repair / error-prone translesion synthesis / mismatch repair / response to UV / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / Termination of translesion DNA synthesis / Recognition of DNA damage by PCNA-containing replication complex / 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 / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / protein-macromolecule adaptor activity / damaged DNA binding / DNA-directed DNA polymerase activity / DNA replication / nucleoplasm / metal ion binding / cytoplasm
Similarity search - Function
DNA repair protein Rev1, C-terminal domain / DNA polymerase delta subunit 3 / DNA polymerase delta subunit 3 superfamily / DNA polymerase subunit Cdc27 / DNA repair protein Rev1, C-terminal / Rev1, C-terminal domain superfamily / : / DNA repair protein REV1 C-terminal domain / DNA repair protein Rev1 / HUWE1/Rev1, ubiquitin binding region ...DNA repair protein Rev1, C-terminal domain / DNA polymerase delta subunit 3 / DNA polymerase delta subunit 3 superfamily / DNA polymerase subunit Cdc27 / DNA repair protein Rev1, C-terminal / Rev1, C-terminal domain superfamily / : / DNA repair protein REV1 C-terminal domain / DNA repair protein Rev1 / HUWE1/Rev1, ubiquitin binding region / Ubiquitin binding region / : / DNA polymerase-iota, thumb domain / BRCA1 C Terminus (BRCT) domain / 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. / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA polymerase delta subunit 3 / DNA repair protein REV1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailsfewest violations, model1
AuthorsPustovalova, Y. / Korzhnev, D.
CitationJournal: Biochemistry / Year: 2016
Title: Interaction between the Rev1 C-Terminal Domain and the PolD3 Subunit of Pol zeta Suggests a Mechanism of Polymerase Exchange upon Rev1/Pol zeta-Dependent Translesion Synthesis.
Authors: Pustovalova, Y. / Magalhaes, M.T. / D'Souza, S. / Rizzo, A.A. / Korza, G. / Walker, G.C. / Korzhnev, D.M.
History
DepositionApr 1, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2016Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA repair protein REV1
B: DNA polymerase delta subunit 3


Theoretical massNumber of molelcules
Total (without water)12,7342
Polymers12,7342
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)20 / 200structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein DNA repair protein REV1 / Alpha integrin-binding protein 80 / AIBP80 / Rev1-like terminal deoxycytidyl transferase


Mass: 10954.614 Da / Num. of mol.: 1 / Fragment: hRev1-CT, unp residues 1158-1251
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: REV1, REV1L / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9UBZ9, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Protein/peptide DNA polymerase delta subunit 3 / DNA polymerase delta subunit p66


Mass: 1779.135 Da / Num. of mol.: 1 / Fragment: unp residues 231-246
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIAA0039, POLD3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15054

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HNCO
1413D HN(CA)CB
1513D HBHA(CO)NH
1613D (H)CCH-TOCSY
1713D CCH-TOCSY
1813D 1H-13C NOESY
1913D 1H-15N NOESY
11012D 1H-1H (filt.) TOCSY
11112D 1H-1H (filt.) NOESY
11213D 1H-13C (CNfilt.) NOESY
11313D 1H-15N (CNfilt.) NOESY

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Sample preparation

DetailsContents: 0.5 mM [U-100% 13C; U-100% 15N] Rev1-CT, 0.5-0.8 mM PolD3, 50 mM potassium phosphate, 100 mM sodium chloride, 2 mM DTT, 0.5 mM EDTA, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
0.5 mMRev1-CT-1[U-100% 13C; U-100% 15N]1
mMPolD3-20.5-0.81
50 mMpotassium phosphate-31
100 mMsodium chloride-41
2 mMDTT-51
0.5 mMEDTA-61
Sample conditionsIonic strength: 100 / pH: 7 / Pressure: ambient / Temperature: 288 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian AvanceVarianAVANCE5001
Varian AvanceVarianAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
NMRPipe5.5Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CARA1.9.0Keller and Wuthrichchemical shift assignment
CARA1.9.0Keller and Wuthrichchemical shift calculation
CARA1.9.0Keller and Wuthrichpeak picking
ABACUS_(CNS)Brunger, Adams, Clore, Gros, Nilges and Readrefinement
TALOS2.2Cornilescu, Delaglio and Baxdata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 20

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