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- PDB-5mlw: Crystal structure of human PCNA in complex with ZRANB3 APIM motif... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5mlw | ||||||
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Title | Crystal structure of human PCNA in complex with ZRANB3 APIM motif peptide | ||||||
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![]() | HYDROLASE / endonuclease / metalloprotein / PCNA / DNA-binding | ||||||
Function / homology | ![]() DNA rewinding / 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 ...DNA rewinding / 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 / negative regulation of DNA recombination / Processive synthesis on the lagging strand / PCNA complex / Removal of the Flap Intermediate / replication fork reversal / 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 / ATP-dependent DNA/DNA annealing activity / ATP-dependent chromatin remodeler activity / K63-linked polyubiquitin modification-dependent protein binding / 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 / helicase activity / 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 / DNA endonuclease activity / 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 / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / 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 / chromosome, telomeric region / damaged DNA binding / Hydrolases; Acting on ester bonds / nuclear body / DNA repair / centrosome / DNA damage response / chromatin binding / protein-containing complex binding / chromatin / enzyme binding / negative regulation of transcription by RNA polymerase II / zinc ion binding / extracellular exosome / nucleoplasm / ATP binding / identical protein binding / nucleus Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ariza, A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural insights into the function of ZRANB3 in replication stress response. Authors: Sebesta, M. / Cooper, C.D.O. / Ariza, A. / Carnie, C.J. / Ahel, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 315.6 KB | Display | ![]() |
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PDB format | ![]() | 259 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 478.4 KB | Display | ![]() |
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Full document | ![]() | 484.5 KB | Display | |
Data in XML | ![]() | 29.5 KB | Display | |
Data in CIF | ![]() | 40.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5mkwC ![]() 5mloC ![]() 1vymS 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
#1: Protein | Mass: 28795.752 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein/peptide | Mass: 1266.510 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) ![]() #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.67 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 100 mM lithium sulfate + 30% (w/v) polyvinylpyrrolidone + 100 mM HEPES pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 12, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2822 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→73.29 Å / Num. obs: 31686 / % possible obs: 100 % / Redundancy: 11.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.104 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 2.45→2.55 Å / Redundancy: 9.7 % / Rmerge(I) obs: 1.297 / Mean I/σ(I) obs: 2 / CC1/2: 0.565 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1VYM Resolution: 2.45→73.29 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.925 / SU B: 25.41 / SU ML: 0.28 / Cross valid method: THROUGHOUT / ESU R: 0.645 / ESU R Free: 0.303 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 66.671 Å2
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Refinement step | Cycle: 1 / Resolution: 2.45→73.29 Å
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Refine LS restraints |
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