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- PDB-2lsj: Solution structure of the mouse Rev1 CTD in complex with the Rev1... -

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Basic information

Entry
Database: PDB / ID: 2lsj
TitleSolution structure of the mouse Rev1 CTD in complex with the Rev1-interacting Region (RIR)of Pol Kappa
Components
  • DNA polymerase kappaPOLK
  • DNA repair protein REV1
KeywordsPROTEIN BINDING/PROTEIN BINDING / Rev1 / RIR / Pol Kappa / Translesion Synthesis / TLS / CTD / PROTEIN BINDING-PROTEIN BINDING complex
Function / homology
Function and homology information


Gap-filling DNA repair synthesis and ligation in GG-NER / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / HDR through Homologous Recombination (HRR) / Termination of translesion DNA synthesis / Dual Incision in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / deoxycytidyl transferase activity ...Gap-filling DNA repair synthesis and ligation in GG-NER / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / HDR through Homologous Recombination (HRR) / Termination of translesion DNA synthesis / Dual Incision in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / deoxycytidyl transferase activity / nucleotide-excision repair, DNA gap filling / error-free translesion synthesis / site of DNA damage / error-prone translesion synthesis / response to UV / cellular response to UV / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / DNA replication / damaged DNA binding / DNA-directed DNA polymerase / molecular adaptor activity / DNA-directed DNA polymerase activity / nuclear body / DNA repair / DNA damage response / nucleoplasm / metal ion binding / nucleus
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 IV ...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 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 repair protein REV1 / DNA polymerase kappa
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
AuthorsLiu, J. / Wojtaszek, J. / Zhou, P.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Multifaceted recognition of vertebrate Rev1 by translesion polymerases zeta and kappa.
Authors: Wojtaszek, J. / Liu, J. / D'Souza, S. / Wang, S. / Xue, Y. / Walker, G.C. / Zhou, P.
History
DepositionMay 1, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 20, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / 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_software.name / _struct_ref_seq_dif.details
Revision 1.3May 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)16,2632
Polymers16,2632
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 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein DNA repair protein REV1 / / Rev1-like terminal deoxycytidyl transferase


Mass: 13271.145 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rev1, Rev1l / Plasmid: pMAL-C2 / Production host: Escherichia coli (E. coli)
References: UniProt: Q920Q2, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Protein/peptide DNA polymerase kappa / POLK / DINB protein / DINP


Mass: 2992.351 Da / Num. of mol.: 1 / Fragment: Rev1-interacting Region (RIR)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / References: UniProt: Q9QUG2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC
1323D HNCA
1423D HN(CO)CA
1523D HN(CA)CB
1623D HN(COCA)CB
1723D HA(CA)NH
1823D HA(CACO)NH
1923D HNCO
11023D (HCA)CO(CA)NH
11134D (H)CCH-TOCSY
11234D H(CCO)NH-TOCSY
11313D 1H-15N NOESY
11433D 1H-13C NOESY
11524D 13C-HMQC-NOESY-15N-HSQC
11634D 13C-HMQC-NOESY-13C-HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.7-1 mM [U-100% 15N] protein, 0.7-1 mM [U-100% 15N] peptide, 25 mM sodium phosphate, 100 mM potassium chloride, 10 mM DTT, 1 mM EDTA, 90% H2O/10% D2O90% H2O/10% D2O
20.7-1 mM [U-100% 13C; U-100% 15N] protein, 0.7-1 mM [U-100% 13C; U-100% 15N] peptide, 25 mM sodium phosphate, 100 mM potassium chloride, 10 mM DTT, 1 mM EDTA, 90% H2O/10% D2O90% H2O/10% D2O
30.7-1 mM [U-100% 13C; U-100% 15N] protein, 0.7-1 mM [U-100% 13C; U-100% 15N] peptide, 25 mM sodium phosphate, 100 mM potassium chloride, 10 mM DTT, 1 mM EDTA, 100% D2O100% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMentity_1-1[U-100% 15N]0.7-11
mMentity_2-2[U-100% 15N]0.7-11
25 mMsodium phosphate-31
100 mMpotassium chloride-41
10 mMDTT-51
1 mMEDTA-61
mMentity_1-7[U-100% 13C; U-100% 15N]0.7-12
mMentity_2-8[U-100% 13C; U-100% 15N]0.7-12
25 mMsodium phosphate-92
100 mMpotassium chloride-102
10 mMDTT-112
1 mMEDTA-122
mMentity_1-13[U-100% 13C; U-100% 15N]0.7-13
mMentity_2-14[U-100% 13C; U-100% 15N]0.7-13
25 mMsodium phosphate-153
100 mMpotassium chloride-163
10 mMDTT-173
1 mMEDTA-183
Sample conditionsIonic strength: 0.1 / pH: 7.0 / Pressure: ambient / Temperature: 310 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
NameDeveloperClassification
TALOSCornilescu, Delaglio and Baxdata analysis
SparkyGoddarddata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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