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- PDB-6axd: Structures of REV1 UBM2 domain complex with ubiquitin and with th... -

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Basic information

Entry
Database: PDB / ID: 6axd
TitleStructures of REV1 UBM2 domain complex with ubiquitin and with the first small-molecule that inhibits the REV1 UBM2-ubiquitin interaction
ComponentsDNA repair protein REV1
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / ubiquitin-binding motif / STRUCTURAL PROTEIN / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


deoxycytidyl transferase activity / error-free translesion synthesis / error-prone translesion synthesis / response to UV / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / Termination of translesion DNA synthesis / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / DNA replication ...deoxycytidyl transferase activity / error-free translesion synthesis / error-prone translesion synthesis / response to UV / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / Termination of translesion DNA synthesis / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / DNA replication / damaged DNA binding / DNA-directed DNA polymerase activity / nucleoplasm / metal ion binding
Similarity search - Function
DNA repair protein Rev1, C-terminal / Rev1, C-terminal domain superfamily / : / DNA repair protein REV1 C-terminal domain / DNA repair protein Rev1 / HUWE1/Rev1, ubiquitin binding region / Ubiquitin binding region / : / DNA polymerase-iota, thumb domain / BRCA1 C Terminus (BRCT) domain ...DNA repair protein Rev1, C-terminal / Rev1, C-terminal domain superfamily / : / DNA repair protein REV1 C-terminal domain / DNA repair protein Rev1 / HUWE1/Rev1, ubiquitin binding region / Ubiquitin binding region / : / DNA polymerase-iota, thumb domain / 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 / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
DNA repair protein REV1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsFujii, N. / Vanarotti, M.
CitationJournal: J. Mol. Biol. / Year: 2018
Title: Structures of REV1 UBM2 Domain Complex with Ubiquitin and with a Small-Molecule that Inhibits the REV1 UBM2-Ubiquitin Interaction.
Authors: Vanarotti, M. / Grace, C.R. / Miller, D.J. / Actis, M.L. / Inoue, A. / Evison, B.J. / Vaithiyalingam, S. / Singh, A.P. / McDonald, E.T. / Fujii, N.
History
DepositionSep 6, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 8, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model

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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)7,8141
Polymers7,8141
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area3110 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20structures with the least restraint violations
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: 7813.632 Da / Num. of mol.: 1 / Fragment: residues 998-1040
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: REV1, REV1L
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
References: UniProt: Q9UBZ9, 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
112anisotropic12D 1H-15N HSQC
121anisotropic13D HNCA
131anisotropic13D HN(CA)CB
141anisotropic23D (H)CCH-TOCSY
152anisotropic13D 1H-15N NOESY
161anisotropic12D 1H-13C HSQC

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution10.5 mM [U-13C; U-15N] REV1 UBM2, 20mM sodium phosphate, 100 mM NacL, pH 7.0, 90% H2O/10% D2O20 mM sodium phosphate, 100 mM NaCl, ph 7.013C15NUBM290% H2O/10% D2O
solution20.5 mM [U-99% 15N] REV1 UBM2, 20mM sodium phosphate, 100 mM NacL, pH 7.0, 90% H2O/10% D2O20 mM sodium phosphate, 100 mM NaCl, ph 7.015NUBM290% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMREV1 UBM2[U-13C; U-15N]1
0.5 mMREV1 UBM2[U-99% 15N]2
Sample conditionsDetails: 20mM soidium phosphate, 100 mM NacL, pH 7.0 / Ionic strength: 0.5 mM / Label: 20mM sodium phosphate, 100 mM NacL, pH 7.0 / pH: 7 / Pressure: 1 mbar / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE8002

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Processing

NMR software
NameVersionClassification
CYANA2.1refinement
CYANA2.1structure solution
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 20 / Conformers submitted total number: 20

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