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- PDB-6eht: Modulation of PCNA sliding surface by p15PAF suggests a suppressi... -
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Basic information
Entry | Database: PDB / ID: 6eht | ||||||
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Title | Modulation of PCNA sliding surface by p15PAF suggests a suppressive mechanism for cisplatin-induced DNA lesion bypass by pol eta holoenzyme | ||||||
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![]() | DNA BINDING PROTEIN / Structural analysis / human PCNA P15 DNA macro complex | ||||||
Function / homology | ![]() positive regulation of deoxyribonuclease activity / dinucleotide insertion or deletion binding / PCNA-p21 complex / mitotic telomere maintenance via semi-conservative replication / purine-specific mismatch base pair DNA N-glycosylase activity / nuclear lamina / MutLalpha complex binding / positive regulation of DNA-directed DNA polymerase activity / Polymerase switching / Telomere C-strand (Lagging Strand) Synthesis ...positive regulation of deoxyribonuclease activity / dinucleotide insertion or deletion binding / PCNA-p21 complex / mitotic telomere maintenance via semi-conservative replication / purine-specific mismatch base pair DNA N-glycosylase activity / nuclear lamina / MutLalpha complex binding / positive regulation of DNA-directed DNA polymerase activity / Polymerase switching / Telomere C-strand (Lagging Strand) Synthesis / Processive synthesis on the lagging strand / PCNA complex / Removal of the Flap Intermediate / Processive synthesis on the C-strand of the telomere / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Polymerase switching on the C-strand of the telomere / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / Transcription of E2F targets under negative control by DREAM complex / Removal of the Flap Intermediate from the C-strand / replisome / centrosome cycle / response to L-glutamate / histone acetyltransferase binding / DNA polymerase processivity factor activity / G1/S-Specific Transcription / leading strand elongation / response to dexamethasone / replication fork processing / nuclear replication fork / SUMOylation of DNA replication proteins / estrous cycle / PCNA-Dependent Long Patch Base Excision Repair / cyclin-dependent protein kinase holoenzyme complex / mismatch repair / translesion synthesis / response to cadmium ion / DNA polymerase binding / response to UV / epithelial cell differentiation / positive regulation of DNA repair / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / base-excision repair, gap-filling / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / replication fork / positive regulation of DNA replication / male germ cell nucleus / liver regeneration / nuclear estrogen receptor binding / Recognition of DNA damage by PCNA-containing replication complex / Termination of translesion DNA synthesis / Translesion Synthesis by POLH / HDR through Homologous Recombination (HRR) / Dual Incision in GG-NER / receptor tyrosine kinase binding / cellular response to hydrogen peroxide / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / cellular response to UV / cellular response to xenobiotic stimulus / E3 ubiquitin ligases ubiquitinate target proteins / response to estradiol / heart development / DNA replication / chromosome, telomeric region / damaged DNA binding / molecular adaptor activity / nuclear body / regulation of cell cycle / centrosome / DNA damage response / chromatin binding / protein-containing complex binding / chromatin / perinuclear region of cytoplasm / enzyme binding / negative regulation of transcription by RNA polymerase II / extracellular exosome / nucleoplasm / identical protein binding / nucleus Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | De March, M. / Barrera-Vilarmau, S. / Mentegari, E. / Merino, N. / Bressan, E. / Maga, G. / Crehuet, R. / Onesti, S. / Blanco, F.J. / De Biasio, A. | ||||||
![]() | ![]() Title: p15PAF binding to PCNA modulates the DNA sliding surface. Authors: De March, M. / Barrera-Vilarmau, S. / Crespan, E. / Mentegari, E. / Merino, N. / Gonzalez-Magana, A. / Romano-Moreno, M. / Maga, G. / Crehuet, R. / Onesti, S. / Blanco, F.J. / De Biasio, A. #1: ![]() Title: Structure of p15(PAF)-PCNA complex and implications for clamp sliding during DNA replication and repair. Authors: De Biasio, A. / de Opakua, A.I. / Mortuza, G.B. / Molina, R. / Cordeiro, T.N. / Castillo, F. / Villate, M. / Merino, N. / Delgado, S. / Gil-Carton, D. / Luque, I. / Diercks, T. / Bernado, P. ...Authors: De Biasio, A. / de Opakua, A.I. / Mortuza, G.B. / Molina, R. / Cordeiro, T.N. / Castillo, F. / Villate, M. / Merino, N. / Delgado, S. / Gil-Carton, D. / Luque, I. / Diercks, T. / Bernado, P. / Montoya, G. / Blanco, F.J. #2: ![]() Title: Structural basis of human PCNA sliding on DNA. Authors: De March, M. / Merino, N. / Barrera-Vilarmau, S. / Crehuet, R. / Onesti, S. / Blanco, F.J. / De Biasio, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Download
PDBx/mmCIF format | ![]() | 319 KB | Display | ![]() |
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PDB format | ![]() | 252.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 474.8 KB | Display | ![]() |
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Full document | ![]() | 491.6 KB | Display | |
Data in XML | ![]() | 30.6 KB | Display | |
Data in CIF | ![]() | 41.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6gwsC ![]() 4d2gS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
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Components
-Proliferating cell nuclear ... , 2 types, 3 molecules ABC
#1: Protein | Mass: 28036.033 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | | Mass: 28287.336 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() References: UniProt: P12004 |
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-DNA chain , 2 types, 2 molecules FG
#4: DNA chain | Mass: 3109.053 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
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#5: DNA chain | Mass: 2979.968 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
-Protein/peptide / Non-polymers , 2 types, 11 molecules DE![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#3: Protein/peptide | Mass: 2362.834 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.36 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 10% polyethylene glycol 3350 0.1 M sodium acetate pH 4.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 7, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→46.12 Å / Num. obs: 14271 / % possible obs: 95.3 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.105 / Net I/av σ(I): 4.5 / Net I/σ(I): 5.7 |
Reflection shell | Resolution: 3.2→3.37 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2122 / % possible all: 98.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4D2G Resolution: 3.2→40.48 Å / Cor.coef. Fo:Fc: 0.835 / Cor.coef. Fo:Fc free: 0.806 / SU B: 91.608 / SU ML: 0.68 / Cross valid method: THROUGHOUT / ESU R Free: 0.721 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 63.479 Å2
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Refinement step | Cycle: 1 / Resolution: 3.2→40.48 Å
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Refine LS restraints |
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