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- PDB-2lsi: Solution structure of polymerase-interacting domain of human Rev1... -

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Basic information

Entry
Database: PDB / ID: 2lsi
TitleSolution structure of polymerase-interacting domain of human Rev1 in complex with translesional synthesis polymerase kappa
Components
  • DNA polymerase kappa
  • DNA repair protein REV1
KeywordsTRANSFERASE / polymerase-interacting domain / Rev1 / polymerase kappa / Rev1-interacting motif
Function / homology
Function and homology information


deoxycytidyl transferase activity / nucleotide-excision repair, DNA gap filling / error-free translesion synthesis / error-prone translesion synthesis / 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 ...deoxycytidyl transferase activity / nucleotide-excision repair, DNA gap filling / error-free translesion synthesis / error-prone translesion synthesis / 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 / HDR through Homologous Recombination (HRR) / Dual Incision in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / cellular response to UV / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / DNA replication / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nuclear body / DNA repair / DNA damage response / nucleoplasm / nucleus / metal ion binding / cytosol
Similarity search - Function
DNA repair protein Rev1, C-terminal domain / DNA repair protein Rev1, C-terminal / Rev1, C-terminal domain superfamily / : / DNA repair protein REV1 C-terminal domain / HUWE1/Rev1, ubiquitin binding region / Ubiquitin binding region / Rad18-like CCHC zinc finger / DNA repair protein Rev1 / DNA polymerase type-Y, HhH motif ...DNA repair protein Rev1, C-terminal domain / DNA repair protein Rev1, C-terminal / Rev1, C-terminal domain superfamily / : / DNA repair protein REV1 C-terminal domain / HUWE1/Rev1, ubiquitin binding region / Ubiquitin binding region / Rad18-like CCHC zinc finger / DNA repair protein Rev1 / DNA polymerase type-Y, HhH motif / IMS family HHH motif / DNA polymerase IV / DNApol eta/Rev1, HhH motif / Rad18, zinc finger UBZ4-type / Zinc finger UBZ4-type profile. / 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 kappa / DNA repair protein REV1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, explicit water refinement
Model detailslowest energy, model1
AuthorsLiu, D. / Ryu, K. / Ko, J. / Choi, B.
CitationJournal: To be Published
Title: Insights into the scaffold mechanism of human Rev1 in translesional synthesis revealed by the structural studies on its polymerase-interacting domain
Authors: Liu, D. / Ryu, K. / Ko, J. / Choi, B.
History
DepositionMay 1, 2012Deposition site: BMRB / Processing site: PDBJ
Revision 1.0May 29, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA repair protein REV1
B: DNA polymerase kappa


Theoretical massNumber of molelcules
Total (without water)13,6092
Polymers13,6092
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)15 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 11449.201 Da / Num. of mol.: 1
Fragment: Protein interaction domain, UNP RESIDUES 1156-1251
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: REV1, REV1L / Production host: Escherichia coli (E. coli)
References: UniProt: Q9UBZ9, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Protein/peptide DNA polymerase kappa / DINB protein / DINP


Mass: 2159.493 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 562-577 / Source method: obtained synthetically / Details: The peptide was chemically synthesized. / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9UBT6, DNA-directed DNA polymerase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-13C NOESY aromatic
1213D 1H-13C NOESY aliphatic
1313D 1H-15N NOESY
1413D (H)CCH-TOCSY
1513D H(CCO)NH
1613D CBCA(CO)NH
1713D HN(CA)CB
1813D HNCO
1913D HBHA(CO)NH
11013D (H)CCH-COSY

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Sample preparation

DetailsContents: 0.8mM [U-99% 13C; U-99% 15N] entity-1, 50mM Bis-Tris-2, 100 mM NaCl-3, 1mM DTT-4, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMentity-1[U-99% 13C; U-99% 15N]1
50 mMBis-Tris-21
100 mMNaCl-31
1 mMDTT-41
Sample conditionsIonic strength: 0.1 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE9002

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
Xplorrefinement
RefinementMethod: simulated annealing, explicit water refinement / Software ordinal: 1
NMR constraintsProtein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 92 / Protein psi angle constraints total count: 92
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 15 / Representative conformer: 1

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