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- PDB-2m2i: NMR solution structure of BRCT domain of yeast REV1 -

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Basic information

Entry
Database: PDB / ID: 2m2i
TitleNMR solution structure of BRCT domain of yeast REV1
ComponentsDNA repair protein REV1
KeywordsTRANSFERASE / BRCT / REV1
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 / : / DNA polymerase-iota, thumb 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 ...DNA repair protein Rev1 / BRCT domain / : / DNA polymerase-iota, thumb 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
Model detailsclosest to the average, model 10
AuthorsPustovalova, Y. / Maciejewski, M.W. / Korzhnev, D.M.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: NMR mapping of PCNA interaction with translesion synthesis DNA polymerase Rev1 mediated by Rev1-BRCT domain.
Authors: Pustovalova, Y. / Maciejewski, M.W. / Korzhnev, D.M.
History
DepositionDec 21, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Database references
Revision 1.2Feb 5, 2014Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_software
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
Revision 1.4May 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


Theoretical massNumber of molelcules
Total (without water)10,7931
Polymers10,7931
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 / 100target function
RepresentativeModel #1closest to the average

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Components

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


Mass: 10792.604 Da / Num. of mol.: 1 / Fragment: BRCT domain (UNP residues 158-251)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: REV1 / 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-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1312D 1H-13C HSQC aromatic
1413D HNCA
1513D HN(CO)CA
1613D HN(CA)CB
1713D CBCA(CO)NH
1813D HNCO
1913D C(CO)NH
11013D HBHA(CO)NH
11113D (H)CCH-TOCSY
11213D CCH-TOCSY
11313D (H)CCH-TOCSY-aro
11413D 1H-13C NOESY
11513D 1H-15N NOESY
11613D 1H-13C NOESY aromatic

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Sample preparation

DetailsContents: 70 uM [U-99% 13C; U-99% 15N] Rev1-BRCT, 50 mM potassium phosphate, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.070 mMRev1-BRCT-1[U-99% 13C; U-99% 15N]1
50 mMpotassium phosphate-21
Sample conditionsIonic strength: 0 / pH: 7 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian VNMRSVarianVNMRS8001
Varian VNMRSVarianVNMRS6002
Varian VNMRSVarianVNMRS5003

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Processing

NMR software
NameVersionDeveloperClassification
Rowland_NMR_Toolkit3.1Jeffrey C. Hochprocessing
Rowland_NMR_Toolkit3.1Alan S. Sternprocessing
VnmrJVariancollection
XEASYBartels et al.data analysis
XEASYBartels et al.peak picking
XEASYBartels et al.chemical shift assignment
TALOS+Cornilescu, Delaglio and Baxdihedral angle restraints
TALOS+Shen, Delaglio, Cornilescu, and Baxdihedral angle restraints
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1816 / NOE intraresidue total count: 459 / NOE long range total count: 619 / NOE medium range total count: 308 / NOE sequential total count: 424 / Protein phi angle constraints total count: 66 / Protein psi angle constraints total count: 70
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20
NMR ensemble rmsDistance rms dev: 0.0151 Å / Distance rms dev error: 0.0015 Å

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