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- PDB-7t1b: Rev1 Ternary Complex with rCTP and Ca2+ -

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Basic information

Entry
Database: PDB / ID: 7t1b
TitleRev1 Ternary Complex with rCTP and Ca2+
Components
  • DNA (5'-D(*AP*TP*CP*GP*CP*TP*AP*CP*CP*AP*CP*AP*CP*CP*CP*C)-3')
  • DNA (5'-D(P*GP*GP*GP*GP*TP*GP*TP*GP*GP*TP*AP*G)-3')
  • DNA repair protein REV1
KeywordsTRANSFERASE/DNA / DNA polymerase / REPLICATION / TRANSFERASE-DNA complex
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 / : / DNA polymerase-iota, thumb domain / BRCT domain / DNA polymerase, Y-family, little finger domain / MutS, DNA mismatch repair protein, domain I - #60 / MutS, DNA mismatch repair protein, domain I / DNA polymerase, Y-family, little finger domain / impB/mucB/samB family C-terminal domain / UmuC domain ...DNA repair protein Rev1 / : / DNA polymerase-iota, thumb domain / BRCT domain / DNA polymerase, Y-family, little finger domain / MutS, DNA mismatch repair protein, domain I - #60 / MutS, DNA mismatch repair protein, domain I / 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 / Dna Ligase; domain 1 / 5' to 3' exonuclease, C-terminal subdomain / DNA polymerase; domain 1 / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
CYTIDINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA repair protein REV1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsFreudenthal, B.D. / Weaver, T.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Nat Commun / Year: 2022
Title: Mechanism of nucleotide discrimination by the translesion synthesis polymerase Rev1.
Authors: Weaver, T.M. / Click, T.H. / Khoang, T.H. / Todd Washington, M. / Agarwal, P.K. / Freudenthal, B.D.
History
DepositionDec 1, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
P: DNA (5'-D(P*GP*GP*GP*GP*TP*GP*TP*GP*GP*TP*AP*G)-3')
T: DNA (5'-D(*AP*TP*CP*GP*CP*TP*AP*CP*CP*AP*CP*AP*CP*CP*CP*C)-3')
A: DNA repair protein REV1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8087
Polymers60,1533
Non-polymers6554
Water6,449358
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6230 Å2
ΔGint-66 kcal/mol
Surface area23710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.193, 73.541, 117.674
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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DNA chain , 2 types, 2 molecules PT

#1: DNA chain DNA (5'-D(P*GP*GP*GP*GP*TP*GP*TP*GP*GP*TP*AP*G)-3')


Mass: 3814.474 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(*AP*TP*CP*GP*CP*TP*AP*CP*CP*AP*CP*AP*CP*CP*CP*C)-3')


Mass: 5052.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Protein , 1 types, 1 molecules A

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


Mass: 51285.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: REV1, YOR346W, O6339 / Production host: Escherichia coli (E. coli)
References: UniProt: P12689, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases

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Non-polymers , 4 types, 362 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CTP / CYTIDINE-5'-TRIPHOSPHATE


Mass: 483.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O14P3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 358 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 15-23% PEG3350, 200 mM ammonium nitrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jan 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.75→25 Å / Num. obs: 77480 / % possible obs: 98.1 % / Redundancy: 2.5 % / Biso Wilson estimate: 19.63 Å2 / CC1/2: 0.997 / Net I/σ(I): 11.46
Reflection shellResolution: 1.75→1.78 Å / Num. unique obs: 2549 / CC1/2: 0.452

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5WM1

5wm1


Resolution: 1.75→24.63 Å / SU ML: 0.1788 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.6913
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2281 3245 4.19 %
Rwork0.1829 74235 -
obs0.1848 77480 73.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.3 Å2
Refinement stepCycle: LAST / Resolution: 1.75→24.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3475 571 37 358 4441
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00874307
X-RAY DIFFRACTIONf_angle_d1.05485956
X-RAY DIFFRACTIONf_chiral_restr0.0629667
X-RAY DIFFRACTIONf_plane_restr0.0066665
X-RAY DIFFRACTIONf_dihedral_angle_d20.86941670
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.770.236580.3073188X-RAY DIFFRACTION4.31
1.78-1.80.2447220.3452507X-RAY DIFFRACTION11.56
1.8-1.830.3834380.2895864X-RAY DIFFRACTION19.97
1.83-1.860.3282610.28281418X-RAY DIFFRACTION32.39
1.86-1.90.3344840.27711889X-RAY DIFFRACTION42.61
1.9-1.930.2631990.23222193X-RAY DIFFRACTION50.13
1.93-1.970.25081060.21962403X-RAY DIFFRACTION55.3
1.97-2.020.24771220.20872689X-RAY DIFFRACTION61.16
2.02-2.060.23421340.20673060X-RAY DIFFRACTION69.57
2.06-2.120.20521440.18183393X-RAY DIFFRACTION77.33
2.12-2.170.23471660.18473731X-RAY DIFFRACTION85.14
2.17-2.240.24861760.19624045X-RAY DIFFRACTION92
2.24-2.310.28541780.19864193X-RAY DIFFRACTION95.67
2.31-2.390.27971940.20664339X-RAY DIFFRACTION98.67
2.39-2.490.25031920.20984349X-RAY DIFFRACTION99.37
2.49-2.60.26071920.2064353X-RAY DIFFRACTION99.41
2.6-2.740.30721930.20334373X-RAY DIFFRACTION99.43
2.74-2.910.27421890.20164369X-RAY DIFFRACTION99.54
2.91-3.130.20461880.19074345X-RAY DIFFRACTION99.5
3.13-3.450.24461900.16144379X-RAY DIFFRACTION99.59
3.45-3.940.17631900.15274374X-RAY DIFFRACTION99.98
3.94-4.960.16161930.14374389X-RAY DIFFRACTION99.96
4.96-24.630.22491860.17874392X-RAY DIFFRACTION99.91

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