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- PDB-7t1a: Rev1 Ternary Complex with dATP and Ca2+ -

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Basic information

Entry
Database: PDB / ID: 7t1a
TitleRev1 Ternary Complex with dATP 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(*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 / metal ion binding / nucleus / 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 / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2'-DEOXYADENOSINE 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: 1.81 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(*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)60,8568
Polymers60,1533
Non-polymers7045
Water5,513306
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6510 Å2
ΔGint-78 kcal/mol
Surface area23680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.136, 73.336, 115.446
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(*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, 311 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-DTP / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE


Mass: 491.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O12P3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 306 / 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: 2.19 Å3/Da / Density % sol: 43.74 %
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 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.8→25 Å / Num. obs: 55331 / % possible obs: 99.3 % / Redundancy: 3.5 % / Biso Wilson estimate: 20.05 Å2 / CC1/2: 0.997 / Net I/σ(I): 12.53
Reflection shellResolution: 1.8→1.83 Å / Num. unique obs: 2406 / CC1/2: 0.556

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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 6X6Z

6x6z


Resolution: 1.81→24.65 Å / SU ML: 0.2409 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.4409
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2296 2912 5.26 %
Rwork0.1931 52419 -
obs0.1951 55331 59.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.11 Å2
Refinement stepCycle: LAST / Resolution: 1.81→24.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3478 568 39 306 4391
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01334364
X-RAY DIFFRACTIONf_angle_d1.27816046
X-RAY DIFFRACTIONf_chiral_restr0.061670
X-RAY DIFFRACTIONf_plane_restr0.0072674
X-RAY DIFFRACTIONf_dihedral_angle_d22.2761670
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.81-1.830.385450.317983X-RAY DIFFRACTION1.99
1.84-1.870.274790.3147174X-RAY DIFFRACTION4.11
1.87-1.90.3468200.3278348X-RAY DIFFRACTION8.33
1.9-1.940.3499350.2914636X-RAY DIFFRACTION15.2
1.94-1.980.284520.3025933X-RAY DIFFRACTION22.05
1.98-2.020.3523720.29461269X-RAY DIFFRACTION30.03
2.02-2.070.2775910.26681620X-RAY DIFFRACTION38.35
2.07-2.120.23461080.25021888X-RAY DIFFRACTION44.94
2.12-2.180.24751260.24942166X-RAY DIFFRACTION51.09
2.18-2.240.32671260.22952346X-RAY DIFFRACTION55.6
2.24-2.310.27471380.21822576X-RAY DIFFRACTION60.85
2.31-2.390.28271490.21912835X-RAY DIFFRACTION66.97
2.39-2.490.31741730.2123155X-RAY DIFFRACTION74.47
2.49-2.60.26651950.21653526X-RAY DIFFRACTION83.94
2.6-2.740.24312240.21953978X-RAY DIFFRACTION94.34
2.74-2.910.25242330.22854071X-RAY DIFFRACTION96.63
2.91-3.140.26832300.21624144X-RAY DIFFRACTION98.14
3.14-3.450.24522380.17434189X-RAY DIFFRACTION98.77
3.45-3.950.19942310.15664156X-RAY DIFFRACTION99.05
3.95-4.970.17112230.14284157X-RAY DIFFRACTION98.52
4.97-24.650.1722340.18094169X-RAY DIFFRACTION98.55

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