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- PDB-7jkl: Human PrimPol misinserting dATP opposite the 8-oxoguanine lesion ... -

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Basic information

Entry
Database: PDB / ID: 7jkl
TitleHuman PrimPol misinserting dATP opposite the 8-oxoguanine lesion (3'-end base of the primer strand is 2',3'-dideoxy-terminated).
Components
  • DNA (5'-D(*GP*GP*GP*TP*GP*TP*GP*GP*TP*AP*GP*CP*(DDG))-3')
  • DNA (5'-D(P*AP*(8OG)P*CP*GP*CP*TP*AP*CP*CP*AP*CP*AP*CP*CP*CP*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


DNA primase AEP / R-loop processing / mitochondrial DNA replication / DNA primase activity / mitochondrial DNA repair / replication fork processing / error-prone translesion synthesis / translesion synthesis / DNA-directed RNA polymerase complex / response to UV ...DNA primase AEP / R-loop processing / mitochondrial DNA replication / DNA primase activity / mitochondrial DNA repair / replication fork processing / error-prone translesion synthesis / translesion synthesis / DNA-directed RNA polymerase complex / response to UV / 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 / 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: 2.384 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 28, 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

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Assembly

Deposited unit
A: DNA-directed primase/polymerase protein
C: DNA (5'-D(P*AP*(8OG)P*CP*GP*CP*TP*AP*CP*CP*AP*CP*AP*CP*CP*CP*C)-3')
D: DNA (5'-D(*GP*GP*GP*TP*GP*TP*GP*GP*TP*AP*GP*CP*(DDG))-3')
B: DNA-directed primase/polymerase protein
G: DNA (5'-D(P*AP*(8OG)P*CP*GP*CP*TP*AP*CP*CP*AP*CP*AP*CP*CP*CP*C)-3')
H: DNA (5'-D(*GP*GP*GP*TP*GP*TP*GP*GP*TP*AP*GP*CP*(DDG))-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,69613
Polymers100,4096
Non-polymers1,2877
Water1,892105
1
A: DNA-directed primase/polymerase protein
C: DNA (5'-D(P*AP*(8OG)P*CP*GP*CP*TP*AP*CP*CP*AP*CP*AP*CP*CP*CP*C)-3')
D: DNA (5'-D(*GP*GP*GP*TP*GP*TP*GP*GP*TP*AP*GP*CP*(DDG))-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8286
Polymers50,2043
Non-polymers6233
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA-directed primase/polymerase protein
G: DNA (5'-D(P*AP*(8OG)P*CP*GP*CP*TP*AP*CP*CP*AP*CP*AP*CP*CP*CP*C)-3')
H: DNA (5'-D(*GP*GP*GP*TP*GP*TP*GP*GP*TP*AP*GP*CP*(DDG))-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8687
Polymers50,2043
Non-polymers6634
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.525, 65.641, 74.307
Angle α, β, γ (deg.)69.440, 83.430, 87.740
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*(8OG)P*CP*GP*CP*TP*AP*CP*CP*AP*CP*AP*CP*CP*CP*C)-3')


Mass: 5078.291 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*GP*GP*GP*TP*GP*TP*GP*GP*TP*AP*GP*CP*(DDG))-3')


Mass: 4087.657 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 112 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.: 3 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 105 / 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: 2.33 Å3/Da / Density % sol: 47.17 %
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: 0.97921 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 2.37→69.17 Å / Num. obs: 33664 / % possible obs: 91.2 % / Redundancy: 3.5 % / CC1/2: 0.993 / Rmerge(I) obs: 0.108 / Net I/σ(I): 7
Reflection shellResolution: 2.37→2.46 Å / Redundancy: 2.9 % / Num. unique obs: 2495 / CC1/2: 0.449 / % possible all: 64

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5L2X

5l2x


Resolution: 2.384→69.17 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 33.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.277 1615 4.9 %
Rwork0.2197 31339 -
obs0.2224 32954 91.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 446.73 Å2 / Biso mean: 82.6032 Å2 / Biso min: 34.13 Å2
Refinement stepCycle: final / Resolution: 2.384→69.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4159 1143 115 105 5522
Biso mean--63.69 61.87 -
Num. residues----576
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055626
X-RAY DIFFRACTIONf_angle_d0.4977832
X-RAY DIFFRACTIONf_chiral_restr0.038863
X-RAY DIFFRACTIONf_plane_restr0.002799
X-RAY DIFFRACTIONf_dihedral_angle_d17.7173052
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.384-2.45370.3856960.3856175961
2.4537-2.53290.40941400.3588263093
2.5329-2.62340.33061470.3233270194
2.6234-2.72850.34681630.3028278197
2.7285-2.85270.32351240.2602278196
2.8527-3.00310.31481400.2323271296
3.0031-3.19120.27651330.2272269894
3.1912-3.43760.2921290.2369275595
3.4376-3.78350.29581500.2041261493
3.7835-4.33090.27411190.1954261290
4.3309-5.45620.23421390.1801265093
5.4562-69.170.23231350.1977264692

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