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- PDB-7jl8: Human PrimPol extending from the correct primer base C opposite t... -

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Basic information

Entry
Database: PDB / ID: 7jl8
TitleHuman PrimPol extending from the correct primer base C opposite the 8-oxoguanine lesion
Components
  • DNA (5'-D(P*AP*TP*(8OG)P*CP*CP*TP*AP*CP*CP*AP*CP*A)-3')
  • DNA (5'-D(P*GP*TP*GP*GP*TP*AP*GP*GP*C)-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


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 ...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 / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / manganese ion binding / 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: 2.1 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*A)-3')
D: DNA (5'-D(P*GP*TP*GP*GP*TP*AP*GP*GP*C)-3')
B: DNA-directed primase/polymerase protein
G: DNA (5'-D(P*AP*TP*(8OG)P*CP*CP*TP*AP*CP*CP*AP*CP*A)-3')
H: DNA (5'-D(P*GP*TP*GP*GP*TP*AP*GP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,33420
Polymers100,3916
Non-polymers1,94314
Water2,900161
1
A: DNA-directed primase/polymerase protein
C: DNA (5'-D(P*AP*TP*(8OG)P*CP*CP*TP*AP*CP*CP*AP*CP*A)-3')
D: DNA (5'-D(P*GP*TP*GP*GP*TP*AP*GP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,18510
Polymers50,1953
Non-polymers9907
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*A)-3')
H: DNA (5'-D(P*GP*TP*GP*GP*TP*AP*GP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,14910
Polymers50,1953
Non-polymers9547
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.689, 65.330, 72.001
Angle α, β, γ (deg.)68.470, 85.670, 86.920
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*A)-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*GP*TP*AP*GP*GP*C)-3')


Mass: 4103.655 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 6 types, 175 molecules

#4: Chemical ChemComp-DTP / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / Deoxyadenosine 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.: 3 / Source method: obtained synthetically / Formula: Ca
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.2 Å3/Da / Density % sol: 44.15 %
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 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03324 Å / Relative weight: 1
ReflectionResolution: 2.099→28.162 Å / Num. obs: 48622 / % possible obs: 97.1 % / Redundancy: 3.4 % / CC1/2: 0.998 / Net I/σ(I): 11.6
Reflection shellResolution: 2.1→2.16 Å / Num. unique obs: 3825 / CC1/2: 0.78 / % possible all: 93.6

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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: 2.1→28.16 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 23.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2133 2308 4.75 %
Rwork0.1871 46258 -
obs0.1883 48566 97.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 220.87 Å2 / Biso mean: 65.1446 Å2 / Biso min: 26.2 Å2
Refinement stepCycle: final / Resolution: 2.1→28.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4059 807 217 161 5244
Biso mean--65.11 48.93 -
Num. residues----560
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.150.32161430.29182749289294
2.15-2.20.30271460.25812906305297
2.2-2.250.26431710.2362865303697
2.25-2.310.26711410.22752878301997
2.31-2.380.27091490.22122865301497
2.38-2.460.24961470.21142865301297
2.46-2.540.28021560.20572908306497
2.54-2.650.24491470.19962895304297
2.65-2.770.25051390.19382916305597
2.77-2.910.24021330.18992860299397
2.91-3.090.20321370.19412934307198
3.09-3.330.20331410.18372914305598
3.33-3.670.20331400.16662957309798
3.67-4.20.16581320.16492922305498
4.2-5.280.16131290.1562925305498
5.28-28.160.21991570.19882899305698
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)
13.00830.26510.03132.8605-0.37970.3781-0.43710.3574-0.858-0.62950.05321.03410.5642-0.711-0.54150.0384-0.1274-0.63440.3660.19180.830740.8304-60.1254-3.0686
23.03021.69271.06063.3262-0.8842.3289-0.0497-0.09360.6405-0.23020.21680.8322-0.188-0.0158-0.10540.28860.0277-0.06570.34010.02960.596248.2849-52.01833.2347
32.8350.0119-0.93463.03250.0051.53670.1131-0.41230.13510.4663-0.04010.036-0.23270.1367-0.09060.4117-0.02690.02640.3551-0.05890.30559.4003-62.803521.9404
42.5995-0.3362-0.78233.65580.50833.44260.20960.0914-0.11390.1782-0.00110.03230.01270.1587-0.1930.3928-0.01130.01780.3774-0.06670.414758.9373-71.598112.8234
53.00844.33241.29097.28290.06794.33970.3313-0.79280.36371.7172-0.47590.91710.3134-0.71690.08240.8634-0.15520.14040.5702-0.0650.374551.9867-70.593830.5708
62.3159-0.0502-0.20633.5674-0.66151.06330.0726-0.14780.2670.2984-0.08880.3935-0.0819-0.05370.00770.37670.00640.04350.4046-0.08440.381958.3582-53.341213.472
71.6021-1.98740.0342.77080.72671.66-0.03490.2645-0.1124-0.28240.1584-0.4120.31210.1168-0.08150.484-0.0020.04340.4749-0.06790.489862.903-69.17325.6305
82.57730.8145-1.23154.60552.02471.98880.9097-0.9967-0.32460.5555-0.58420.42211.3288-0.3279-0.56410.7149-0.3714-0.26930.8550.19141.046534.7253-72.288917.4444
92.7171.0463-0.76393.5237-0.85370.35050.34690.0885-0.4106-1.75350.66451.83071.7954-1.0092-0.67181.7145-0.5511-0.04820.950.18831.423433.926-74.631219.4316
104.2602-0.97020.61723.98460.01543.37590.26010.3365-0.2597-0.17750.00840.67790.1714-0.6852-0.16830.2649-0.0083-0.050.5299-0.01270.485649.9217-93.5894-12.7374
113.293-0.93880.98433.67750.32821.3437-0.07850.2086-0.47540.0285-0.00110.19060.3664-0.2733-0.00710.25760.0189-0.05120.3402-0.05840.325559.91-99.1122-11.924
123.4486-0.934-1.80142.04790.09922.8579-0.1134-0.0918-0.25820.11180.0483-0.1035-0.02270.24780.05190.2580.0115-0.02840.359-0.02650.321379.7993-87.9533-5.6929
134.4012-0.6864-0.85233.84441.20192.76250.0678-0.33480.19230.19620.01460.1936-0.1352-0.1864-0.08010.3130.0282-0.04170.3302-0.03190.327770.8619-79.2544-2.9889
142.61840.7933-0.86561.91710.02581.7166-0.0080.0704-0.0642-0.1544-0.0158-0.18360.03890.17610.05750.26970.0557-0.02170.4084-0.02850.340676.3245-91.4289-8.78
151.78980.57370.33732.49761.69462.00520.0684-0.17420.29840.3275-0.05390.2802-0.2592-0.0996-0.10180.43810.03210.06640.4294-0.05810.420965.1973-81.22991.8863
162.5997-1.4724-0.58941.6377-1.16443.3419-0.2830.57290.7457-1.3575-0.1789-0.5584-0.95870.5980.33770.912-0.1863-0.03140.79110.25070.59669.0525-78.2781-28.0604
173.0442-1.67010.27829.1677-1.10653.2178-0.02040.93470.0739-2.51620.30750.6846-0.922-0.1532-0.13681.3471-0.09220.07030.84680.30830.900668.6532-76.0963-30.8217
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 172 )A103 - 172
4X-RAY DIFFRACTION4chain 'A' and (resid 173 through 192 )A173 - 192
5X-RAY DIFFRACTION5chain 'A' and (resid 193 through 280 )A193 - 280
6X-RAY DIFFRACTION6chain 'A' and (resid 281 through 330 )A281 - 330
7X-RAY DIFFRACTION7chain 'A' and (resid 331 through 348 )A331 - 348
8X-RAY DIFFRACTION8chain 'C' and (resid 2 through 13 )C2 - 13
9X-RAY DIFFRACTION9chain 'D' and (resid 6 through 14 )D6 - 14
10X-RAY DIFFRACTION10chain 'B' and (resid 38 through 58 )B38 - 58
11X-RAY DIFFRACTION11chain 'B' and (resid 59 through 102 )B59 - 102
12X-RAY DIFFRACTION12chain 'B' and (resid 103 through 172 )B103 - 172
13X-RAY DIFFRACTION13chain 'B' and (resid 173 through 192 )B173 - 192
14X-RAY DIFFRACTION14chain 'B' and (resid 193 through 330 )B193 - 330
15X-RAY DIFFRACTION15chain 'B' and (resid 331 through 348 )B331 - 348
16X-RAY DIFFRACTION16chain 'G' and (resid 3 through 12 )G3 - 12
17X-RAY DIFFRACTION17chain 'H' and (resid 6 through 14 )H6 - 14

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