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- PDB-7r3y: The crystal structure of the V426L variant of Pol2CORE in complex... -

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Basic information

Entry
Database: PDB / ID: 7r3y
TitleThe crystal structure of the V426L variant of Pol2CORE in complex with DNA and an incoming nucleotide
Components
  • (DNA Template) x 2
  • DNA Primer
  • DNA polymerase epsilon catalytic subunit
KeywordsDNA BINDING PROTEIN / protein-DNA complex
Function / homology2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / DNA / DNA (> 10) / :
Function and homology information
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsBarbari, S.R. / Beach, A.K. / Markgren, J.G. / Parkash, V. / Johansson, E. / Shcherbakova, P.V.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Cancerfonden Sweden
CitationJournal: Nucleic Acids Res. / Year: 2022
Title: Enhanced polymerase activity permits efficient synthesis by cancer-associated DNA polymerase ε variants at low dNTP levels.
Authors: Barbari, S.R. / Beach, A.K. / Markgren, J.G. / Parkash, V. / Moore, E.A. / Johansson, E. / Shcherbakova, P.V.
History
DepositionFeb 8, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 27, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: 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
A: DNA polymerase epsilon catalytic subunit
P: DNA Primer
T: DNA Template
B: DNA polymerase epsilon catalytic subunit
C: DNA Primer
D: DNA Template
hetero molecules


Theoretical massNumber of molelcules
Total (without water)290,97412
Polymers289,8316
Non-polymers1,1436
Water23413
1
A: DNA polymerase epsilon catalytic subunit
P: DNA Primer
T: DNA Template
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,4956
Polymers144,9243
Non-polymers5713
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6500 Å2
ΔGint-44 kcal/mol
Surface area50720 Å2
MethodPISA
2
B: DNA polymerase epsilon catalytic subunit
C: DNA Primer
D: DNA Template
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,4796
Polymers144,9083
Non-polymers5713
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6320 Å2
ΔGint-44 kcal/mol
Surface area50910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.400, 70.100, 159.500
Angle α, β, γ (deg.)90.000, 113.100, 90.000
Int Tables number3
Space group name H-MP121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein DNA polymerase epsilon catalytic subunit


Mass: 136725.188 Da / Num. of mol.: 2 / Fragment: Catalytic subunit of DNA Pol Epsilon / Mutation: V426L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: PACBIOSEQ_LOCUS4978 / Plasmid: pET 28a / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: A0A7I9C3S1, DNA-directed DNA polymerase

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DNA chain , 3 types, 4 molecules PCTD

#2: DNA chain DNA Primer


Mass: 3293.174 Da / Num. of mol.: 2 / Fragment: DNA primer / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA Template


Mass: 4905.177 Da / Num. of mol.: 1 / Fragment: DNA Template / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA Template


Mass: 4889.177 Da / Num. of mol.: 1 / Fragment: DNA Template / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 19 molecules

#5: Chemical ChemComp-DTP / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE


Mass: 491.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O12P3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.65 Å3/Da / Density % sol: 53.55 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 50mM MES pH6.5, PEG20K,2.5% glycerol, 150mM Sodium Actetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 4, 2017
RadiationMonochromator: Si (111), double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.6→47.84 Å / Num. obs: 96815 / % possible obs: 99.5 % / Redundancy: 3.409 % / Biso Wilson estimate: 80.264 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.075 / Rrim(I) all: 0.089 / Χ2: 1.036 / Net I/σ(I): 9.21 / Num. measured all: 330071 / Scaling rejects: 72
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.6-2.83.4241.4940.756568719247191860.481.77499.7
2.8-3.13.4640.6151.857017120315202580.8560.72999.7
3.1-3.53.3760.2114.945862817478173640.9840.25299.3
3.5-4.53.4310.07113.917200621105209860.9970.08499.4
4.5-63.4140.04122.313726210988109140.9980.04999.3
6-103.290.02825.6920766637363110.9990.03499
10-153.0130.02231.813769125912510.9990.02699.4
15-47.843.270.0231.117825825450.9990.02493.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.18.2_3874refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 4m8o

4m8o


Resolution: 2.6→47.84 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 35.37 / Stereochemistry target values: ML / Details: TLS refinement using Phenix.Refine
RfactorNum. reflection% reflection
Rfree0.2702 4826 5 %
Rwork0.2203 91628 -
obs0.2227 96454 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 237.35 Å2 / Biso mean: 98.4605 Å2 / Biso min: 44.97 Å2
Refinement stepCycle: final / Resolution: 2.6→47.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17689 1059 64 13 18825
Biso mean--63.79 69.97 -
Num. residues----2259
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6-2.630.39831580.406630103168100
2.63-2.660.41511620.391930683230100
2.66-2.690.37051610.38953050321199
2.69-2.730.3971580.372130033161100
2.73-2.760.40151610.361630383199100
2.76-2.80.40531620.360930893251100
2.8-2.840.37951590.33823001316099
2.84-2.880.34181600.33643035319599
2.88-2.930.40511620.33493075323799
2.93-2.980.341600.31530293189100
2.98-3.030.33161620.30230773239100
3.03-3.080.34061600.29323009316999
3.08-3.140.31171600.281630483208100
3.14-3.210.31281590.26933055321499
3.21-3.280.31191580.26333016317499
3.28-3.350.29721590.2483068322799
3.35-3.440.30941580.2392991314999
3.44-3.530.29371610.24793054321599
3.53-3.630.31181600.23943036319699
3.63-3.750.29921610.213530543215100
3.75-3.880.29651620.21673086324899
3.88-4.040.24751610.2023056321799
4.04-4.220.23991610.186530523213100
4.22-4.440.24511630.17633092325599
4.45-4.720.20361610.1683059322099
4.72-5.090.22861630.176130943257100
5.09-5.60.23121610.18083071323299
5.6-6.410.27391650.19963120328599
6.41-8.070.26511630.19563104326799
8.07-47.840.2031650.18483088325395
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)
10.8859-1.04760.39781.7278-0.0631.79540.27961.0844-0.1932-0.3528-0.11480.30550.334-0.13320.00250.92960.13810.1680.83370.03010.5282-40.53557.2839127.2671
2-0.02930.18680.08971.42320.60020.2323-0.085-0.16030.0862-0.22490.01480.1217-0.17050.05250.00010.91260.09920.00880.7160.13030.9442-46.550286.9629141.9415
32.6487-0.88430.2181.8937-0.16591.53520.1110.2752-0.1891-0.2496-0.1428-0.48620.34130.54730.00030.80420.12660.1590.6661-0.02710.74-22.450748.3847141.7222
41.5305-0.33670.55121.9013-0.8061.8261-0.1438-0.56190.16220.35250.0575-0.2757-0.1033-0.3081-0.00270.7390.0633-0.01820.713-0.07450.6092-41.409859.282172.7174
52.785-0.0919-0.00011.0557-0.14212.024-0.0008-0.15550.08090.2771-0.0242-0.76030.1450.4294-0.00070.83990.0988-0.2220.86090.01431.1593-7.503350.4441175.3753
60.2735-0.2064-0.25120.33470.11520.31640.0655-1.35580.50060.749-0.316-0.5595-0.7205-0.42280.00230.9837-0.0166-0.22321.1947-0.22931.2601-16.980965.1757174.8283
70.473-0.0465-0.18341.29210.55480.5109-0.3359-0.31740.50120.25290.0579-1.1414-0.610.24760.00040.8888-0.0965-0.26310.8484-0.01151.3062-20.345665.803169.3541
82.82550.06570.9272.125-0.31442.19060.2682-0.9015-0.18360.2996-0.3712-0.58210.30920.1304-0.02030.8424-0.11160.13350.9417-0.09980.548940.233794.8146237.9782
9-0.00660.2046-0.11271.8043-0.6460.94180.0735-0.13540.27710.2122-0.171-0.1067-0.24910.1541-0.00050.815-0.0516-0.01940.7175-0.11250.965443.9592114.0418226.3954
103.23790.90840.65591.9209-0.17531.92270.1343-0.3903-0.06480.1723-0.13210.46140.3588-0.6299-0.00560.7683-0.08530.11890.6961-0.05710.731619.109583.0276223.734
112.60360.61031.45091.62390.78182.4593-0.14610.95010.1601-0.28360.02160.18720.01130.4725-0.02150.70330.0220.00190.99140.03750.655834.207289.0063192.2686
121.7535-0.8654-0.12051.38830.52641.704-0.0561-0.07030.1949-0.1426-0.00790.6036-0.0388-0.4148-0.00090.8106-0.083-0.17641.1091-0.14261.2217-1.829289.0318195.9919
130.33970.153-0.31850.414-0.17030.282-0.24811.01920.4508-0.6019-0.27110.7948-0.81140.2686-0.00130.9410.0431-0.33041.24610.07121.52114.201999.7694193.1681
140.65290.1722-0.31051.3719-0.46380.6445-0.66620.23790.1346-0.23320.18371.0489-1.0748-0.32720.00130.88420.1279-0.28460.9220.04231.329517.6848100.4208198.5193
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 31 through 137 )A31 - 137
2X-RAY DIFFRACTION2chain 'A' and (resid 138 through 234 )A138 - 234
3X-RAY DIFFRACTION3chain 'A' and (resid 235 through 511 )A235 - 511
4X-RAY DIFFRACTION4chain 'A' and (resid 512 through 943 )A512 - 943
5X-RAY DIFFRACTION5chain 'A' and (resid 944 through 1186 )A944 - 1186
6X-RAY DIFFRACTION6chain 'P' and (resid 1 through 10 )P1 - 10
7X-RAY DIFFRACTION7chain 'T' and (resid 2 through 16 )T2 - 16
8X-RAY DIFFRACTION8chain 'B' and (resid 31 through 148 )B31 - 148
9X-RAY DIFFRACTION9chain 'B' and (resid 149 through 274 )B149 - 274
10X-RAY DIFFRACTION10chain 'B' and (resid 275 through 547 )B275 - 547
11X-RAY DIFFRACTION11chain 'B' and (resid 548 through 1031 )B548 - 1031
12X-RAY DIFFRACTION12chain 'B' and (resid 1032 through 1186 )B0
13X-RAY DIFFRACTION13chain 'C' and (resid 1 through 10 )C1 - 10
14X-RAY DIFFRACTION14chain 'D' and (resid 2 through 16 )D2 - 16

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