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- PDB-6x6z: Rev1 Ternary Complex with dCTP and Ca2+ -

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Basic information

Entry
Database: PDB / ID: 6x6z
TitleRev1 Ternary Complex with dCTP and Ca2+
Components
  • DNA (5'-D(*CP*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
KeywordsREPLICATION/DNA / DNA polymerase / REPLICATION / REPLICATION-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 / 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. ...DNA repair protein Rev1 / 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
Similarity search - Domain/homology
2'-DEOXYCYTIDINE-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: 1.4 Å
AuthorsWeaver, T.M. / Freudenthal, B.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Visualizing Rev1 catalyze protein-template DNA synthesis.
Authors: Weaver, T.M. / Cortez, L.M. / Khoang, T.H. / Washington, M.T. / Agarwal, P.K. / Freudenthal, B.D.
History
DepositionMay 29, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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(*CP*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)59,8528
Polymers59,1733
Non-polymers6795
Water13,763764
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6440 Å2
ΔGint-80 kcal/mol
Surface area23770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.376, 73.947, 117.290
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(*CP*AP*TP*CP*GP*CP*TP*AP*CP*CP*AP*CP*AP*CP*CP*CP*C)-3')


Mass: 5037.278 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: 50320.887 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, 769 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 467.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O13P3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 764 / 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: 2.31 Å3/Da / Density % sol: 46.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 15-23% PEG3350 and 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 PILATUS3 R 200K-A / Detector: PIXEL / Date: Jul 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.4→35.26 Å / Num. obs: 198840 / % possible obs: 99.5 % / Redundancy: 4 % / Biso Wilson estimate: 16.24 Å2 / Rrim(I) all: 0.07 / Net I/σ(I): 25.4
Reflection shellResolution: 1.4→1.5998 Å / Num. unique obs: 63131 / CC1/2: 0.426

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WM1

5wm1


Resolution: 1.4→35.26 Å / SU ML: 0.1644 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.4508
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2074 3751 1.89 %
Rwork0.1865 195089 -
obs0.1869 198840 96.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.41 Å2
Refinement stepCycle: LAST / Resolution: 1.4→35.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3482 572 37 764 4855
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00844325
X-RAY DIFFRACTIONf_angle_d0.99875984
X-RAY DIFFRACTIONf_chiral_restr0.0781667
X-RAY DIFFRACTIONf_plane_restr0.0053669
X-RAY DIFFRACTIONf_dihedral_angle_d19.80381669
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.420.2971180.32246002X-RAY DIFFRACTION80.14
1.42-1.440.30631350.3116838X-RAY DIFFRACTION91.37
1.44-1.460.32711280.30116872X-RAY DIFFRACTION91.58
1.46-1.480.32261360.29047004X-RAY DIFFRACTION92.81
1.48-1.50.28271390.27736994X-RAY DIFFRACTION94.24
1.5-1.520.25121400.26267159X-RAY DIFFRACTION94.68
1.52-1.550.291340.24977150X-RAY DIFFRACTION95.75
1.55-1.570.24051410.24317251X-RAY DIFFRACTION96.28
1.57-1.60.26571390.23357290X-RAY DIFFRACTION97.09
1.6-1.630.22641460.22277284X-RAY DIFFRACTION97.33
1.63-1.670.25951370.21797290X-RAY DIFFRACTION97.15
1.67-1.70.22661450.20697302X-RAY DIFFRACTION97.42
1.7-1.740.22961350.20537331X-RAY DIFFRACTION97.51
1.74-1.790.27361450.20987324X-RAY DIFFRACTION97.44
1.79-1.830.27261370.20547287X-RAY DIFFRACTION97.26
1.83-1.890.25621400.2177330X-RAY DIFFRACTION97.21
1.89-1.950.20761410.19237308X-RAY DIFFRACTION97.35
1.95-2.020.19891420.17777253X-RAY DIFFRACTION97.35
2.02-2.10.20231400.17087329X-RAY DIFFRACTION97.38
2.1-2.20.19521460.16397319X-RAY DIFFRACTION97.44
2.2-2.310.1961400.17257374X-RAY DIFFRACTION98
2.31-2.460.20471350.18027373X-RAY DIFFRACTION98.57
2.46-2.650.18971430.18227424X-RAY DIFFRACTION99.28
2.65-2.910.21861440.18557504X-RAY DIFFRACTION99.88
2.91-3.330.20171390.17357508X-RAY DIFFRACTION99.84
3.33-4.20.15061410.14847491X-RAY DIFFRACTION99.91
4.2-35.260.18711450.16597498X-RAY DIFFRACTION99.86

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