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- PDB-5n85: Structure of RPA70N in complex with PrimPol (fragment 514-525) -

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Basic information

Entry
Database: PDB / ID: 5n85
TitleStructure of RPA70N in complex with PrimPol (fragment 514-525)
Components
  • DNA-directed primase/polymerase protein
  • Replication protein A 70 kDa DNA-binding subunit
KeywordsPROTEIN BINDING / Complex / Replication / Basic cleft
Function / homology
Function and homology information


DNA primase AEP / protein localization to chromosome / DNA replication factor A complex / R-loop processing / mitochondrial DNA replication / single-stranded telomeric DNA binding / chromatin-protein adaptor activity / : / G-rich strand telomeric DNA binding / protein localization to site of double-strand break ...DNA primase AEP / protein localization to chromosome / DNA replication factor A complex / R-loop processing / mitochondrial DNA replication / single-stranded telomeric DNA binding / chromatin-protein adaptor activity / : / G-rich strand telomeric DNA binding / protein localization to site of double-strand break / Removal of the Flap Intermediate / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / Removal of the Flap Intermediate from the C-strand / HDR through Single Strand Annealing (SSA) / mitochondrial DNA repair / Impaired BRCA2 binding to RAD51 / replication fork processing / site of DNA damage / Presynaptic phase of homologous DNA pairing and strand exchange / PCNA-Dependent Long Patch Base Excision Repair / Activation of the pre-replicative complex / Regulation of HSF1-mediated heat shock response / HSF1 activation / error-prone translesion synthesis / telomere maintenance via telomerase / mismatch repair / translesion synthesis / SUMOylation of DNA damage response and repair proteins / Activation of ATR in response to replication stress / response to UV / telomere maintenance / DNA-directed RNA polymerase complex / Translesion synthesis by REV1 / Translesion synthesis by POLK / replication fork / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / meiotic cell cycle / nucleotide-excision repair / Fanconi Anemia Pathway / Termination of translesion DNA synthesis / Recognition of DNA damage by PCNA-containing replication complex / double-strand break repair via homologous recombination / Translesion Synthesis by POLH / G2/M DNA damage checkpoint / base-excision repair / PML body / HDR through Homologous Recombination (HRR) / Meiotic recombination / Dual Incision in GG-NER / DNA-templated DNA replication / Formation of Incision Complex in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / single-stranded DNA binding / site of double-strand break / manganese ion binding / Processing of DNA double-strand break ends / DNA recombination / Regulation of TP53 Activity through Phosphorylation / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / chromosome, telomeric region / DNA replication / mitochondrial matrix / DNA repair / DNA damage response / chromatin binding / mitochondrion / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
DNA-directed primase/polymerase protein / Herpesviridae UL52/UL70 DNA primase / Replication factor-A protein 1, N-terminal domain / Replication factor A protein 1 / Replication factor-A protein 1, N-terminal / Replication protein A, OB domain / Replication protein A OB domain / : / Replication factor A, C-terminal / Replication factor-A C terminal domain ...DNA-directed primase/polymerase protein / Herpesviridae UL52/UL70 DNA primase / Replication factor-A protein 1, N-terminal domain / Replication factor A protein 1 / Replication factor-A protein 1, N-terminal / Replication protein A, OB domain / Replication protein A OB domain / : / Replication factor A, C-terminal / Replication factor-A C terminal domain / DNA primase, small subunit / DNA primase small subunit / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Replication protein A 70 kDa DNA-binding subunit / DNA-directed primase/polymerase protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBrissett, N.C. / Doherty, A.J.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/H019723/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/M008800/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/M004236/1 United Kingdom
CitationJournal: Nat Commun / Year: 2017
Title: Molecular basis for PrimPol recruitment to replication forks by RPA.
Authors: Guilliam, T.A. / Brissett, N.C. / Ehlinger, A. / Keen, B.A. / Kolesar, P. / Taylor, E.M. / Bailey, L.J. / Lindsay, H.D. / Chazin, W.J. / Doherty, A.J.
History
DepositionFeb 23, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 17, 2024Group: 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: Replication protein A 70 kDa DNA-binding subunit
B: DNA-directed primase/polymerase protein


Theoretical massNumber of molelcules
Total (without water)15,1852
Polymers15,1852
Non-polymers00
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-3 kcal/mol
Surface area6940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.860, 53.090, 54.630
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Replication protein A 70 kDa DNA-binding subunit / RP-A p70 / Replication factor A protein 1 / RF-A protein 1 / Single-stranded DNA-binding protein


Mass: 13497.728 Da / Num. of mol.: 1 / Mutation: E7R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPA1, REPA1, RPA70 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P27694
#2: Protein/peptide DNA-directed primase/polymerase protein / hPrimpol1 / Coiled-coil domain-containing protein 111


Mass: 1687.671 Da / Num. of mol.: 1 / Fragment: UNP Residues 514-528 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: Q96LW4, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 1.81 Å3/Da / Density % sol: 31.96 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.2 M Ammonium acetate 0.1 M Sodium acetate 4.5 20 % w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: May 7, 2015 / Details: VariMax-HF mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→38.073 Å / Num. all: 7856 / Num. obs: 7856 / % possible obs: 99.6 % / Redundancy: 12.8 % / Biso Wilson estimate: 16.67 Å2 / Rpim(I) all: 0.062 / Rrim(I) all: 0.226 / Rsym value: 0.217 / Net I/av σ(I): 3.4 / Net I/σ(I): 10.9 / Num. measured all: 100895
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2-2.1110.40.75111152411040.2390.790.751398.1
2.11-2.2413.40.6481.21415910580.180.6730.6484.299.5
2.24-2.3913.40.5351.4133689970.1490.5560.5355.299.9
2.39-2.5813.50.4111.9126129350.1140.4270.4116.9100
2.58-2.8313.50.3322.3118158770.0920.3450.3328.6100
2.83-3.1613.40.2253.4106187920.0630.2330.22512.1100
3.16-3.6513.30.1255.993116990.0350.130.12518.8100
3.65-4.4713.20.0828.680926150.0230.0850.08226.3100
4.47-6.3212.70.0817.861324840.0230.0850.08125100
6.32-31.11811.10.0698.632642950.0210.0720.06925.499.4

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Processing

Software
NameVersionClassification
PHENIXrefinement
CrystalCleardata collection
MOSFLM7.1.0data reduction
SCALA3.3.21data scaling
PHASER2.5.6phasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IPC

4ipc


Resolution: 2→31.118 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2275 390 4.98 %
Rwork0.187 7435 -
obs0.1891 7825 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 132.64 Å2 / Biso mean: 26.2015 Å2 / Biso min: 5.6 Å2
Refinement stepCycle: final / Resolution: 2→31.118 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1023 0 0 74 1097
Biso mean---31.23 -
Num. residues----133
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041098
X-RAY DIFFRACTIONf_angle_d0.7851503
X-RAY DIFFRACTIONf_chiral_restr0.048182
X-RAY DIFFRACTIONf_plane_restr0.005196
X-RAY DIFFRACTIONf_dihedral_angle_d14.582709
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0001-2.28940.26941320.19822398253099
2.2894-2.88410.23591230.206224632586100
2.8841-31.12150.20851350.173125742709100
Refinement TLS params.Method: refined / Origin x: 2.6106 Å / Origin y: -1.135 Å / Origin z: -5.2363 Å
111213212223313233
T0.0831 Å2-0.0033 Å2-0.0086 Å2-0.0772 Å20.006 Å2--0.0836 Å2
L0.3953 °2-0.0119 °20.135 °2-0.4354 °2-0.1386 °2--0.8591 °2
S0.0092 Å °-0.0444 Å °0.0546 Å °0.0405 Å °-0.0395 Å °-0.0102 Å °-0.121 Å °0.054 Å °0.0082 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA0 - 120
2X-RAY DIFFRACTION1allW1 - 57
3X-RAY DIFFRACTION1allW58 - 74
4X-RAY DIFFRACTION1allB1 - 12

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