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- PDB-5vx7: Solution NMR structure of the BRCT domain of S. cerevisiae Rev1 -

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Basic information

Entry
Database: PDB / ID: 5vx7
TitleSolution NMR structure of the BRCT domain of S. cerevisiae Rev1
ComponentsDNA repair protein REV1
KeywordsTRANSFERASE / Protein binding / DNA replication / DNA damage response / Translesion DNA synthesis / BRCT domain
Function / homology
Function and homology information


deoxycytidyl transferase activity / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / Termination of translesion DNA synthesis / error-free translesion synthesis / error-prone translesion synthesis / replication fork / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / damaged DNA binding ...deoxycytidyl transferase activity / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / Termination of translesion DNA synthesis / error-free translesion synthesis / error-prone translesion synthesis / replication fork / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / damaged DNA binding / DNA-directed DNA polymerase activity / chromatin / mitochondrion / nucleus / metal ion binding / cytoplasm
Similarity search - Function
DNA repair protein Rev1 / BRCT domain / BRCT domain, a BRCA1 C-terminus 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 ...DNA repair protein Rev1 / BRCT domain / BRCT domain, a BRCA1 C-terminus 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 / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA repair protein REV1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing
AuthorsXu, C. / Cui, G. / Botuyan, M.V. / Mer, G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA132878 United States
CitationJournal: To Be Published
Title: Solution NMR structure of the BRCT domain of S. cerevisiae Rev1
Authors: Xu, C. / Cui, G. / Botuyan, M.V. / Mer, G.
History
DepositionMay 23, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Author supporting evidence / Data collection
Category: pdbx_audit_support / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.2May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA repair protein REV1


Theoretical massNumber of molelcules
Total (without water)10,7041
Polymers10,7041
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein DNA repair protein REV1 / Reversionless protein 1


Mass: 10703.555 Da / Num. of mol.: 1 / Fragment: UNP residues 162-251
Source method: isolated from a genetically manipulated source
Details: N terminal sequence GHM is an expression tag.
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: REV1, YOR346W, O6339 / Plasmid: pTEV / Production host: Escherichia coli (E. coli)
References: UniProt: P12689, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic13D 1H-15N TOCSY
131isotropic13D 1H-15N NOESY
142isotropic12D 1H-15N HSQC
152isotropic12D 1H-13C HSQC
1162isotropic12D 1H-13C HSQC aromatic
162isotropic13D CBCA(CO)NH
172isotropic13D HN(CA)CB
182isotropic13D HBHA(CO)NH
192isotropic13D HNCA
1102isotropic13D HN(CO)CA
1112isotropic13D HNCO
1122isotropic13D H(CCO)NH
1132isotropic13D (H)CCH-TOCSY
1142isotropic13D 1H-13C NOESY
1152isotropic13D 1H-13C NOESY aromatic

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11 mM [U-100% 15N] Rev1-BRCT, 50 mM Sodium phosphate buffer, 50 mM NaCl, 90% H2O/10% D2O15N_sample90% H2O/10% D2O
solution21 mM [U-100% 13C; U-100% 15N] Rev1-BRCT, 50 mM sodium phosphate buffer, 50 mM NaCl, 90% H2O/10% D2O15N_13C_sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMRev1-BRCT[U-100% 15N]1
50 mMSodium phosphate buffernatural abundance1
50 mMNaClnatural abundance1
1 mMRev1-BRCT[U-100% 13C; U-100% 15N]2
50 mMsodium phosphate buffernatural abundance2
50 mMNaClnatural abundance2
Sample conditionsIonic strength: 50 mM NaCl mM / Label: Conditions_1 / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 700 MHz

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
SparkyGoddardprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardchemical shift assignment
TALOSCornilescu, Delaglio and Baxdata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
RefinementMethod: simulated annealing / Software ordinal: 9
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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