+Open data
-Basic information
Entry | Database: PDB / ID: 5n8a | ||||||||||||
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Title | Structure of RPA70N in complex with PrimPol (fragment 480-560) | ||||||||||||
Components |
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Keywords | PROTEIN 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 / chromatin-protein adaptor activity / DNA primase activity / Removal of the Flap Intermediate / single-stranded 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 / chromatin-protein adaptor activity / DNA primase activity / Removal of the Flap Intermediate / single-stranded telomeric DNA binding / protein localization to site of double-strand break / 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 / G-rich strand telomeric DNA binding / HDR through Single Strand Annealing (SSA) / Impaired BRCA2 binding to RAD51 / mitochondrial DNA repair / replication fork processing / site of DNA damage / Presynaptic phase of homologous DNA pairing and strand exchange / telomere maintenance via telomerase / Activation of the pre-replicative complex / PCNA-Dependent Long Patch Base Excision Repair / Regulation of HSF1-mediated heat shock response / HSF1 activation / error-prone translesion synthesis / mismatch repair / translesion synthesis / Activation of ATR in response to replication stress / SUMOylation of DNA damage response and repair proteins / DNA-directed RNA polymerase complex / response to UV / telomere maintenance / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / meiotic cell cycle / replication fork / nucleotide-excision repair / Fanconi Anemia Pathway / Recognition of DNA damage by PCNA-containing replication complex / Termination of translesion DNA synthesis / Translesion Synthesis by POLH / double-strand break repair via homologous recombination / base-excision repair / HDR through Homologous Recombination (HRR) / G2/M DNA damage checkpoint / Dual Incision in GG-NER / DNA-templated DNA replication / PML body / Meiotic recombination / Formation of Incision Complex in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / site of double-strand break / manganese ion binding / single-stranded DNA binding / Processing of DNA double-strand break ends / DNA recombination / DNA replication / Regulation of TP53 Activity through Phosphorylation / chromosome, telomeric region / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / mitochondrial matrix / DNA repair / DNA damage response / chromatin binding / zinc ion binding / nucleoplasm / nucleus / metal ion binding Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.28 Å | ||||||||||||
Authors | Brissett, N.C. / Doherty, A.J. | ||||||||||||
Funding support | United Kingdom, 3items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5n8a.cif.gz | 73.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5n8a.ent.gz | 52.4 KB | Display | PDB format |
PDBx/mmJSON format | 5n8a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5n8a_validation.pdf.gz | 436.7 KB | Display | wwPDB validaton report |
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Full document | 5n8a_full_validation.pdf.gz | 438.3 KB | Display | |
Data in XML | 5n8a_validation.xml.gz | 8.8 KB | Display | |
Data in CIF | 5n8a_validation.cif.gz | 12 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n8/5n8a ftp://data.pdbj.org/pub/pdb/validation_reports/n8/5n8a | HTTPS FTP |
-Related structure data
Related structure data | 5n85C 4ipcS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 11161.771 Da / Num. of mol.: 1 / Fragment: UNP residues 479-559 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PRIMPOL, CCDC111 / Plasmid: pET28a / Production host: Escherichia coli BL21 (bacteria) References: UniProt: Q96LW4, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases |
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#2: Protein | Mass: 13353.598 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 / Plasmid: pET15b / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P27694 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.88 Å3/Da / Density % sol: 34.66 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.2M imidazole malate, 30% w/v PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.91407 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 30, 2014 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.91407 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.28→16.247 Å / Num. all: 29019 / Num. obs: 351864 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 6.431 % / CC1/2: 1 / Rmerge(I) obs: 0.043 / Rrim(I) all: 0.047 / Χ2: 0.984 / Net I/σ(I): 20.01 / Num. measured all: 351864 / Scaling rejects: 8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4IPC Resolution: 1.28→16.247 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.12
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 65.99 Å2 / Biso mean: 21.1988 Å2 / Biso min: 8.69 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.28→16.247 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10
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