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- PDB-7jlg: Human PrimPol extending from the erroneous primer base A opposite... -

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Basic information

Entry
Database: PDB / ID: 7jlg
TitleHuman PrimPol extending from the erroneous primer base A opposite the 8-oxoguanine lesion
Components
  • DNA (5'-D(P*AP*TP*(8OG)P*CP*CP*TP*AP*CP*CP*AP*CP*AP*CP*CP*C)-3')
  • DNA (5'-D(P*GP*TP*GP*TP*GP*GP*TP*AP*GP*GP*A)-3')
  • DNA-directed primase/polymerase protein
KeywordsTRANSFERASE/DNA / Translesion / DNA synthesis / DNA Replication / DNA damage / TRANSFERASE / TRANSFERASE-DNA complex
Function / homology
Function and homology information


DNA primase AEP / R-loop processing / mitochondrial DNA replication / DNA primase activity / mitochondrial DNA repair / replication fork processing / translesion synthesis / error-prone translesion synthesis / response to UV / DNA-directed RNA polymerase complex ...DNA primase AEP / R-loop processing / mitochondrial DNA replication / DNA primase activity / mitochondrial DNA repair / replication fork processing / translesion synthesis / error-prone translesion synthesis / response to UV / DNA-directed RNA polymerase complex / replication fork / manganese ion binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / mitochondrial matrix / chromatin binding / zinc ion binding / nucleus
Similarity search - Function
DNA-directed primase/polymerase protein / Herpesviridae UL52/UL70 DNA primase / DNA primase, small subunit / DNA primase small subunit
Similarity search - Domain/homology
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / DI(HYDROXYETHYL)ETHER / DNA / DNA (> 10) / DNA-directed primase/polymerase protein
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsRechkoblit, O. / Aggarwal, A.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35-GM131780 United States
CitationJournal: Nat Commun / Year: 2021
Title: Structural basis of DNA synthesis opposite 8-oxoguanine by human PrimPol primase-polymerase.
Authors: Rechkoblit, O. / Johnson, R.E. / Gupta, Y.K. / Prakash, L. / Prakash, S. / Aggarwal, A.K.
History
DepositionJul 29, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 14, 2021Group: 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_PubMed / _citation.title / _citation_author.identifier_ORCID
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
A: DNA-directed primase/polymerase protein
C: DNA (5'-D(P*AP*TP*(8OG)P*CP*CP*TP*AP*CP*CP*AP*CP*AP*CP*CP*C)-3')
D: DNA (5'-D(P*GP*TP*GP*TP*GP*GP*TP*AP*GP*GP*A)-3')
B: DNA-directed primase/polymerase protein
G: DNA (5'-D(P*AP*TP*(8OG)P*CP*CP*TP*AP*CP*CP*AP*CP*AP*CP*CP*C)-3')
H: DNA (5'-D(P*GP*TP*GP*TP*GP*GP*TP*AP*GP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,87215
Polymers100,4396
Non-polymers1,4339
Water2,360131
1
A: DNA-directed primase/polymerase protein
C: DNA (5'-D(P*AP*TP*(8OG)P*CP*CP*TP*AP*CP*CP*AP*CP*AP*CP*CP*C)-3')
D: DNA (5'-D(P*GP*TP*GP*TP*GP*GP*TP*AP*GP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7916
Polymers50,2193
Non-polymers5713
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA-directed primase/polymerase protein
G: DNA (5'-D(P*AP*TP*(8OG)P*CP*CP*TP*AP*CP*CP*AP*CP*AP*CP*CP*C)-3')
H: DNA (5'-D(P*GP*TP*GP*TP*GP*GP*TP*AP*GP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0819
Polymers50,2193
Non-polymers8626
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.031, 65.210, 73.115
Angle α, β, γ (deg.)71.360, 84.310, 88.630
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein DNA-directed primase/polymerase protein / hPrimpol1 / Coiled-coil domain-containing protein 111


Mass: 41038.488 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRIMPOL, CCDC111 / Production host: Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: Q96LW4, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases

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DNA chain , 2 types, 4 molecules CGDH

#2: DNA chain DNA (5'-D(P*AP*TP*(8OG)P*CP*CP*TP*AP*CP*CP*AP*CP*AP*CP*CP*C)-3')


Mass: 5053.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*GP*TP*GP*TP*GP*GP*TP*AP*GP*GP*A)-3')


Mass: 4127.681 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 140 molecules

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


Mass: 491.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O12P3
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 2.28 Å3/Da / Density % sol: 46.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 225-250 mM CaCl2, 16-19% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.03324 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03324 Å / Relative weight: 1
ReflectionResolution: 2.07→27.841 Å / Num. obs: 52599 / % possible obs: 97 % / Redundancy: 3.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.069 / Net I/σ(I): 8.8
Reflection shellResolution: 2.07→2.13 Å / Num. unique obs: 4069 / CC1/2: 0.336

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5L2X

5l2x


Resolution: 2.07→26.81 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 27.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2188 2494 4.75 %
Rwork0.2007 50028 -
obs0.2016 52522 96.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 232.69 Å2 / Biso mean: 77.2255 Å2 / Biso min: 33.3 Å2
Refinement stepCycle: final / Resolution: 2.07→26.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4116 1021 133 131 5401
Biso mean--67.82 54.68 -
Num. residues----568
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.07-2.110.4021340.37592726286095
2.11-2.150.34621310.33552787291896
2.15-2.20.34211400.32422746288697
2.2-2.250.32741630.29522754291797
2.25-2.310.31011510.27172754290597
2.31-2.370.32111280.26132770289897
2.37-2.440.26491500.24372835298597
2.44-2.520.24131440.23672744288897
2.52-2.610.28971520.23512790294298
2.61-2.710.22161240.21312827295198
2.71-2.840.2341550.21112808296398
2.84-2.980.27471270.21532791291898
2.98-3.170.23871150.21912836295198
3.17-3.420.21331460.19312814296098
3.42-3.760.19471330.1842756288997
3.76-4.30.20711240.17292799292397
4.3-5.410.15751280.15712745287396
5.41-26.810.18981490.18722746289596
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)
12.72753.2625-1.31999.07340.00972.0568-0.33060.8112-0.2606-0.46320.18250.74940.6181-0.44970.17020.6061-0.041-0.29910.71510.1050.997240.7626-60.9557-2.8116
24.02441.74370.56494.3741-0.08011.5597-0.04420.43290.4244-0.60450.25770.9237-0.1634-0.1366-0.1650.4020.0982-0.04480.4490.12480.672247.5062-52.4563.6156
34.01430.8335-1.1193.2214-0.23924.51830.0902-0.81360.04910.7256-0.06650.0632-0.17150.0596-0.00580.47910.00050.0350.4507-0.00140.342159.0109-65.424822.3687
43.30840.375-0.17375.10810.52253.41560.1597-0.2105-0.13570.3535-0.08570.0181-0.19350.0488-0.0310.48130.03470.03980.44660.020.356260.0544-64.488717.3093
52.68432.6041-0.56647.70511.28626.445-0.0408-1.0834-0.51410.67540.032-0.28590.85460.0765-0.05520.83210.07070.07010.79330.15870.583955.8513-73.461131.3009
63.49631.7881-1.6683.7955-1.69312.23670.2009-0.1920.36470.335-0.14160.4406-0.2608-0.1179-0.10690.57890.04470.08990.5293-0.05140.498956.378-55.769816.3534
74.7147-3.9060.24784.09751.40092.97140.05720.21420.3794-0.40390.1922-0.91150.0306-0.0663-0.280.5759-0.01320.11110.5413-0.08220.599663.1239-68.53765.2031
83.46390.7366-1.68043.70490.8172.16150.8977-0.8463-0.29810.8225-0.74930.94621.02150.2243-0.34780.8761-0.3013-0.14240.90920.24661.100634.2688-76.758518.6542
94.83111.6315-0.69113.664-0.37883.4562-0.056-0.2555-0.7702-0.57280.36091.31590.6350.0684-0.29571.764-0.3380.18581.36790.12211.780235.0926-79.179120.9585
106.40550.52370.04476.6130.73773.82810.1210.0357-0.2099-0.12470.09080.377-0.2436-0.3237-0.11610.3050.0599-0.03310.43660.02610.409654.1996-94.5823-13.8839
112.03670.4728-0.02821.65920.00281.8894-0.0205-0.1291-0.03460.11620.067-0.1271-0.03570.1281-0.03740.39060.09160.01480.45360.00950.427874.7935-89.4723-6.5377
121.90760.7367-0.45852.587-0.17331.7027-0.01270.2508-0.1923-0.10790.0378-0.18850.00390.1351-0.01180.34410.07920.02310.4889-0.010.436376.5862-91.3573-8.9854
131.9825-1.39640.93116.99784.33354.77710.1192-0.26450.22870.6649-0.20740.5793-0.0511-0.6361-0.06630.57020.08210.0920.6314-0.02470.521465.2316-81.41451.9711
140.5459-0.1388-0.65981.3718-0.71231.2198-0.59410.89321.0709-1.82520.10680.0341-1.1870.2653-1.02411.4036-0.2714-0.130.83430.46190.874367.7046-73.0117-31.2186
151.60992.42440.81984.525-0.13452.7253-0.13490.88560.3859-2.575-0.22271.5686-0.16190.71720.11351.5369-0.1506-0.02231.03860.5261.541968.1112-75.8595-31.5007
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 47 )A1 - 47
2X-RAY DIFFRACTION2chain 'A' and (resid 48 through 102 )A48 - 102
3X-RAY DIFFRACTION3chain 'A' and (resid 103 through 146 )A103 - 146
4X-RAY DIFFRACTION4chain 'A' and (resid 147 through 192 )A147 - 192
5X-RAY DIFFRACTION5chain 'A' and (resid 193 through 269 )A193 - 269
6X-RAY DIFFRACTION6chain 'A' and (resid 270 through 330 )A270 - 330
7X-RAY DIFFRACTION7chain 'A' and (resid 331 through 348 )A331 - 348
8X-RAY DIFFRACTION8chain 'C' and (resid 2 through 15 )C2 - 15
9X-RAY DIFFRACTION9chain 'D' and (resid 4 through 14 )D4 - 14
10X-RAY DIFFRACTION10chain 'B' and (resid 38 through 82 )B38 - 82
11X-RAY DIFFRACTION11chain 'B' and (resid 83 through 192 )B83 - 192
12X-RAY DIFFRACTION12chain 'B' and (resid 193 through 330 )B193 - 330
13X-RAY DIFFRACTION13chain 'B' and (resid 331 through 348 )B331 - 348
14X-RAY DIFFRACTION14chain 'G' and (resid 1 through 16 )G1 - 16
15X-RAY DIFFRACTION15chain 'H' and (resid 6 through 14 )H6 - 14

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