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- PDB-2lsg: Solution structure of the mouse Rev1 C-terminal domain -

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Basic information

Entry
Database: PDB / ID: 2lsg
TitleSolution structure of the mouse Rev1 C-terminal domain
ComponentsDNA repair protein REV1
KeywordsPROTEIN BINDING / translesion DNA polymerase / Y-family
Function / homology
Function and homology information


Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / Termination of translesion DNA synthesis / deoxycytidyl transferase activity / error-free translesion synthesis / error-prone translesion synthesis / response to UV / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / damaged DNA binding ...Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / Termination of translesion DNA synthesis / deoxycytidyl transferase activity / error-free translesion synthesis / error-prone translesion synthesis / response to UV / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / damaged DNA binding / DNA-directed DNA polymerase activity / nucleus / metal ion binding
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 / DNA repair protein Rev1 / DNApol eta/Rev1, HhH motif / BRCA1 C Terminus (BRCT) domain ...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 / DNA repair protein Rev1 / DNApol eta/Rev1, HhH motif / 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
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
DepositionApr 30, 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


Theoretical massNumber of molelcules
Total (without water)11,8271
Polymers11,8271
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 #1lowest energy

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Components

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


Mass: 11826.576 Da / Num. of mol.: 1 / Fragment: Protein interaction domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pMAL-C2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q920Q2

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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 HNCO
1423D (HCA)CO(CA)NH
1523D HNCA
1623D HN(CO)CA
1723D HN(CA)CB
1823D HN(COCA)CB
1923D HA(CA)NH
11023D HA(CACO)NH
11113D 1H-15N NOESY
11233D 1H-13C NOESY
11324D H(CCO)NH TOCSY
11434D (H)CCH-TOCSY
11534D 13C-HMQC-NOESY-HSQC
11614D 13C-HMQC-NOESY-15N-HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.9-1 mM [U-100% 15N] protein, 25 mM sodium phosphate, 100 mM potassium chloride, 10 mM DTT, 1 mM PMSF, 1 mM EDTA, 90% H2O/10% D2O90% H2O/10% D2O
20.9-1 mM [U-100% 13C; U-100% 15N] protein, 25 mM sodium phosphate, 100 mM potassium chloride, 10 mM DTT, 1 mM PMSF, 1 mM EDTA, 90% H2O/10% D2O90% H2O/10% D2O
30.9-1 mM [U-100% 13C; U-100% 15N] protein, 25 mM sodium phosphate, 100 mM potassium chloride, 10 mM DTT, 1 mM PMSF, 1 mM EDTA, 100% D2O100% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMentity-1[U-100% 15N]0.9-11
25 mMsodium phosphate-21
100 mMpotassium chloride-31
10 mMDTT-41
1 mMPMSF-51
1 mMEDTA-61
mMentity-7[U-100% 13C; U-100% 15N]0.9-12
25 mMsodium phosphate-82
100 mMpotassium chloride-92
10 mMDTT-102
1 mMPMSF-112
1 mMEDTA-122
mMentity-13[U-100% 13C; U-100% 15N]0.9-13
25 mMsodium phosphate-143
100 mMpotassium chloride-153
10 mMDTT-163
1 mMPMSF-173
1 mMEDTA-183
Sample conditionsIonic strength: 0.1-0.125 / pH: 7.0 / Pressure: ambient / Temperature: 298 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
SparkyGoddarddata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
TALOSCornilescu, Delaglio and Baxdata analysis
XEASYBartels et al.peak picking
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 2262 / NOE intraresidue total count: 610 / NOE long range total count: 441 / NOE medium range total count: 666 / NOE sequential total count: 545 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 80 / Protein psi angle constraints total count: 80
NMR representativeSelection criteria: lowest energy
NMR ensembleAverage torsion angle constraint violation: 3.29 ° / Conformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: 4.97 ° / Maximum upper distance constraint violation: 0.35 Å
NMR ensemble rmsDistance rms dev: 0.19 Å / Distance rms dev error: 0.06 Å

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