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- PDB-5yrq: Crystal structure of Rad5 and Rev1 -

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Basic information

Entry
Database: PDB / ID: 5yrq
TitleCrystal structure of Rad5 and Rev1
ComponentsDNA repair protein RAD5,DNA repair protein REV1
KeywordsDNA BINDING PROTEIN / Rad5 / DNA damage tolerance / E3 ligase / TLS polymerase / Rev1
Function / homology
Function and homology information


error-free postreplication DNA repair / deoxycytidyl transferase activity / free ubiquitin chain polymerization / Y-form DNA binding / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / Termination of translesion DNA synthesis / postreplication repair ...error-free postreplication DNA repair / deoxycytidyl transferase activity / free ubiquitin chain polymerization / Y-form DNA binding / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / Termination of translesion DNA synthesis / postreplication repair / error-free translesion synthesis / ATP-dependent activity, acting on DNA / error-prone translesion synthesis / four-way junction DNA binding / replication fork / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / protein polyubiquitination / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / double-strand break repair / damaged DNA binding / four-way junction helicase activity / DNA-directed DNA polymerase activity / chromosome, telomeric region / DNA repair / chromatin / mitochondrion / zinc ion binding / ATP binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
HIRAN domain / HIRAN domain / HIRAN / : / DNA repair protein Rev1 / : / DNA polymerase-iota, thumb domain / BRCT domain / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) ...HIRAN domain / HIRAN domain / HIRAN / : / DNA repair protein Rev1 / : / DNA polymerase-iota, thumb domain / BRCT domain / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related 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 / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Helicase conserved C-terminal domain / Zinc finger RING-type profile. / Zinc finger, RING-type / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Zinc finger, RING/FYVE/PHD-type / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DNA repair protein REV1 / DNA repair protein RAD5
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.999 Å
AuthorsChen, Z.C. / Zhou, C.Y.
CitationJournal: Nucleic Acids Res. / Year: 2016
Title: Involvement of budding yeast Rad5 in translesion DNA synthesis through physical interaction with Rev1.
Authors: Xu, X. / Lin, A.Y. / Zhou, C.Y. / Blackwell, S.R. / Zhang, Y.R. / Wang, Z.H. / Feng, Q.Q. / Guan, R.F. / Hanna, M.D. / Chen, Z.C. / Xiao, W.
History
DepositionNov 9, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
A: DNA repair protein RAD5,DNA repair protein REV1
B: DNA repair protein RAD5,DNA repair protein REV1
D: DNA repair protein RAD5,DNA repair protein REV1
E: DNA repair protein RAD5,DNA repair protein REV1


Theoretical massNumber of molelcules
Total (without water)67,8134
Polymers67,8134
Non-polymers00
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: immunoprecipitation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9490 Å2
ΔGint-22 kcal/mol
Surface area24450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.589, 49.280, 103.074
Angle α, β, γ (deg.)90.00, 92.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
DNA repair protein RAD5,DNA repair protein REV1 / Radiation sensitivity protein 5 / Revertibility protein 2 / Reversionless protein 1


Mass: 16953.314 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: The Rad5 (5-20) and Rev1 (876-985) coding sequences linked with the flexible linker sequence GGSSSSLVPRGSGGSGGSP
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RAD5, REV2, SNM2, YLR032W, REV1, YOR346W, O6339 / Production host: Escherichia coli 042 (bacteria) / Strain (production host): 042
References: UniProt: P32849, UniProt: P12689, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement, Transferases; Transferring phosphorus- ...References: UniProt: P32849, UniProt: P12689, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O

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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: 43.9 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 18-20% PEG 3350, 100mM potassium citrate, 100mM HEPES, 5mM DTT, pH 7.0
PH range: 7.0-7.5 / Temp details: Homoiothermy

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: liquid nitrogen
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97911 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 38367 / % possible obs: 95.7 % / Redundancy: 3 % / Rmerge(I) obs: 0.184 / Rsym value: 0.086 / Net I/σ(I): 16
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.184 / Mean I/σ(I) obs: 6.2 / % possible all: 89.4

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000v705adata reduction
HKL-2000v705adata scaling
PHASERv7.0phasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.999→29.133 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2463 1911 4.98 %
Rwork0.205 --
obs0.2071 38367 95.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.999→29.133 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4075 0 0 154 4229
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064151
X-RAY DIFFRACTIONf_angle_d0.8155579
X-RAY DIFFRACTIONf_dihedral_angle_d15.4362511
X-RAY DIFFRACTIONf_chiral_restr0.045620
X-RAY DIFFRACTIONf_plane_restr0.006710
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9991-2.04910.27491220.2122303X-RAY DIFFRACTION84
2.0491-2.10450.28621460.20992536X-RAY DIFFRACTION95
2.1045-2.16640.29321310.20942572X-RAY DIFFRACTION95
2.1664-2.23630.25611440.19862548X-RAY DIFFRACTION94
2.2363-2.31620.26911160.21452588X-RAY DIFFRACTION95
2.3162-2.40890.2371360.20292529X-RAY DIFFRACTION94
2.4089-2.51840.31081060.21062566X-RAY DIFFRACTION94
2.5184-2.65110.23211300.21462601X-RAY DIFFRACTION94
2.6511-2.81710.27631520.23362665X-RAY DIFFRACTION99
2.8171-3.03440.24711580.23082696X-RAY DIFFRACTION99
3.0344-3.33940.2811460.23072702X-RAY DIFFRACTION99
3.3394-3.82170.23131440.1932714X-RAY DIFFRACTION99
3.8217-4.81140.20141430.17472700X-RAY DIFFRACTION98
4.8114-29.13570.23211370.19762736X-RAY DIFFRACTION96
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.09660.57950.83856.99621.13393.8038-0.13230.14790.2556-0.31380.0927-0.4501-0.00580.16870.04140.0724-0.0240.00730.1742-0.0230.137840.5583-7.59493.7537
21.756-0.7168-0.11113.09081.76242.3779-0.1582-0.32350.13950.22160.1097-0.14790.11470.08940.03980.14660.0245-0.01240.1362-0.00150.0936.4657-10.890510.5267
31.75061.89260.35162.0855-0.54832.06790.0728-0.3999-0.8239-0.53180.2341-0.35861.59550.87150.00630.52810.16330.02010.1998-0.02790.288837.4073-25.82875.6656
43.44010.4408-0.48638.78365.5728.739-0.2901-0.49870.08010.97920.25690.3050.49570.0711-0.03840.19490.06890.03540.26180.0180.135934.1389-13.298819.4157
50.86581.02560.92482.3540.59137.64850.1750.1288-0.2941-0.1276-0.1805-0.61360.39660.3947-0.0340.23570.06160.08560.1131-0.05050.161928.794-2.301639.7073
62.58741.08660.08042.22512.58373.99330.129-0.2296-0.03210.3412-0.40380.81550.2728-0.62810.27020.15780.0116-0.04570.5575-0.05050.4944-1.62851.366723.6484
78.009-1.6355-0.13398.66522.12089.0434-0.5660.28110.4919-0.4810.44271.5381-1.4122-1.73440.1130.43980.1697-0.0090.63070.01430.77261.618814.597333.7448
82.74020.6397-0.73766.6142.323.716-0.16930.6476-0.4042-0.684-0.24580.97880.2378-0.75440.3110.2214-0.0842-0.05810.3282-0.08280.278210.6241-8.89179.5756
95.0474-4.582-1.36497.66252.67861.9574-0.3089-0.213-0.43450.8338-0.27391.16590.5664-0.84050.41540.2393-0.10160.11770.3046-0.03550.29349.2537-8.769620.3566
102.13380.2586-1.02053.7655-0.54953.4762-0.1659-0.0557-0.12790.00680.13690.01290.2998-0.31690.00790.1116-0.0315-0.00410.1087-0.00670.103820.1682-4.614814.9587
110.16080.87331.17524.28065.87378.01660.0437-0.3937-0.61380.64760.0329-0.75831.79340.0608-0.05550.58740.05490.16310.44780.10120.51825.3167-20.256217.5121
122.49420.6391.46985.81963.92757.0799-0.2327-0.22870.2348-0.120.0935-0.60740.3593-0.38070.18320.64230.0857-0.0430.41620.11860.474129.846-31.42435.5013
139.880.39750.51838.39822.45816.2835-0.0705-0.3847-1.04360.1457-0.0068-0.19410.27520.15850.08570.12530.0340.02910.1612-0.0010.222438.91246.916347.6982
145.1102-0.2154-2.06213.81321.25524.56970.1057-0.08550.1501-0.0490.1042-0.5612-0.71480.4251-0.1660.1833-0.0387-0.01250.1914-0.04330.173441.623721.480145.5915
152.0943-1.1178-1.0453.8372.43934.59060.01620.13550.0603-0.37530.0584-0.2494-0.41650.1657-0.02970.1752-0.04110.02260.13980.0110.101132.839517.126142.8806
161.88380.26660.62153.74884.08287.9677-0.37950.56920.2388-0.56730.36170.1382-0.66850.4078-0.05670.3386-0.1481-0.00370.2610.03760.115734.042222.74736.9191
172.4735-0.0634-1.92962.7211-2.20258.44250.2083-0.20610.1640.4071-0.0708-0.4158-0.43210.4685-0.15180.1693-0.0296-0.0350.0881-0.02680.171129.92977.653912.4723
182.0085-4.78874.52938.15562.05547.37620.33960.4296-0.777-0.28480.2601-0.24991.37230.2658-0.55890.3344-0.01160.01930.2635-0.0850.393349.1932-17.53684.9128
191.74372.92422.49125.74614.09523.54320.1069-0.95890.73570.7883-0.4201-0.56240.03160.73490.26330.2576-0.0939-0.04540.4518-0.04110.385751.1208-5.805810.2156
207.0745-1.4859-3.2764.73341.04035.8436-0.0202-0.03330.33530.067-0.0135-0.0159-0.6957-0.03450.05710.2937-0.0362-0.0280.2588-0.05210.398748.821124.688247.5484
212.013-3.2538-1.65122.01930.49742.0125-0.21570.1822-0.7918-0.03990.076-1.17110.20961.0930.18020.346-0.02270.05620.3696-0.01740.560149.27213.834645.9993
220.7363-0.29141.76212.21272.81672.0057-0.22010.1412-0.37630.101-0.03080.6050.0314-0.29550.18360.1635-0.00970.02710.7904-0.06180.4132-3.49356.020231.0194
232.1342-3.4295-2.02845.75132.36716.6674-0.32830.5922-0.27550.0073-0.13261.00910.464-0.91720.33380.1914-0.0438-0.02140.516-0.08510.50461.5357-4.608717.0085
242.4241-0.08860.32844.8962.16014.3676-0.3443-0.59160.27220.4188-0.08280.8603-0.3913-0.96740.30160.2380.11960.01780.3272-0.08450.25868.817513.153138.749
253.51381.3412-0.2426.4521-0.1214.3051-0.38470.07220.6333-0.35040.06720.3312-1.0694-0.5920.22580.48430.1345-0.0830.18360.05420.233214.041621.830331.7124
261.8136-0.8476-0.07757.0144-1.82692.55830.01740.0756-0.01080.19420.00590.1293-0.1826-0.2617-0.00830.17270.0169-0.0130.1333-0.01350.090920.11558.373240.6663
272.6125-0.9458-0.72194.0536-0.40233.421-0.10030.01690.143-0.6431-0.0271-0.1756-0.20170.04240.14460.27150.01790.0080.1546-0.01290.124820.2249.249731.1882
282.15521.91070.54592.01033.70411.36580.16940.0715-0.0437-0.18670.3760.0778-0.6635-0.3602-0.47830.8572-0.06030.03630.56170.18030.465727.915235.640945.6505
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 873:901)
2X-RAY DIFFRACTION2(chain A and resid 902:944)
3X-RAY DIFFRACTION3(chain A and resid 945:955)
4X-RAY DIFFRACTION4(chain A and resid 956:970)
5X-RAY DIFFRACTION5(chain A and resid 971:985)
6X-RAY DIFFRACTION6(chain B and resid 2:11)
7X-RAY DIFFRACTION7(chain B and resid 12:16)
8X-RAY DIFFRACTION8(chain D and resid 873:903)
9X-RAY DIFFRACTION9(chain D and resid 904:914)
10X-RAY DIFFRACTION10(chain D and resid 915:964)
11X-RAY DIFFRACTION11(chain D and resid 965:977)
12X-RAY DIFFRACTION12(chain D and resid 978:985)
13X-RAY DIFFRACTION13(chain E and resid 874:889)
14X-RAY DIFFRACTION14(chain E and resid 890:912)
15X-RAY DIFFRACTION15(chain E and resid 913:948)
16X-RAY DIFFRACTION16(chain E and resid 949:969)
17X-RAY DIFFRACTION17(chain E and resid 970:985)
18X-RAY DIFFRACTION18(chain A and resid 9:12)
19X-RAY DIFFRACTION19(chain A and resid 13:20)
20X-RAY DIFFRACTION20(chain E and resid 9:11)
21X-RAY DIFFRACTION21(chain E and resid 12:17)
22X-RAY DIFFRACTION22(chain D and resid 2:7)
23X-RAY DIFFRACTION23(chain D and resid 8:16)
24X-RAY DIFFRACTION24(chain B and resid 874:908)
25X-RAY DIFFRACTION25(chain B and resid 909:922)
26X-RAY DIFFRACTION26(chain B and resid 923:947)
27X-RAY DIFFRACTION27(chain B and resid 948:976)
28X-RAY DIFFRACTION28(chain B and resid 977:985)

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