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- PDB-1vyj: Structural and biochemical studies of human PCNA complexes provid... -
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Basic information
Entry | Database: PDB / ID: 1vyj | ||||||
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Title | Structural and biochemical studies of human PCNA complexes provide the basis for association with CDK/cyclin and rationale for inhibitor design | ||||||
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![]() | DNA BINDING PROTEIN / DNA / REPLICATION / PROCESSIVITY / ONCOGENE / DNA-BINDING PROTEIN / DNA REPLICATION / DNA-BINDING SYSTEMIC LUPUS ERYTHEMATOSUS | ||||||
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 / 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 / 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 / chromosome, telomeric region / damaged DNA binding / nuclear body / centrosome / chromatin binding / protein-containing complex binding / chromatin / enzyme binding / negative regulation of transcription by RNA polymerase II / extracellular exosome / nucleoplasm / identical protein binding / nucleus Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kontopidis, G. / Wu, S. / Zheleva, D. / Taylor, P. / Mcinnes, C. / Lane, D. / Fischer, P. / Walkinshaw, M.D. | ||||||
![]() | ![]() Title: Structural and Biochemical Studies of Human Proliferating Cell Nuclear Antigen Complexes Provide a Rationale for Cyclin Association and Inhibitor Design Authors: Kontopidis, G. / Wu, S. / Zheleva, D. / Taylor, P. / Mcinnes, C. / Lane, D. / Fischer, P. / Walkinshaw, M.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 326.3 KB | Display | ![]() |
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PDB format | ![]() | 267.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 536.1 KB | Display | ![]() |
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Full document | ![]() | 617.8 KB | Display | |
Data in XML | ![]() | 68.7 KB | Display | |
Data in CIF | ![]() | 92.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1vymC ![]() 1w60C ![]() 1axcS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 28795.752 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein/peptide | Mass: 1908.266 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Water | ChemComp-HOH / | Compound details | THIS PROTEIN IS AN AUXILIARY PROTEIN OF DNA POLYMERASE DELTA IS INVOLVED IN THE CONTROL OF ...THIS PROTEIN IS AN AUXILIARY PROTEIN OF DNA POLYMERASE | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.16 Å3/Da / Density % sol: 60.7 % |
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Crystal grow | pH: 8 / Details: 2.7M AS, HEPES PH8, pH 8.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Date: Aug 15, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8456 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→30 Å / Num. obs: 62908 / % possible obs: 98.7 % / Observed criterion σ(I): 0 / Redundancy: 8.2 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 2.8→2.85 Å / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 1 / % possible all: 98.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1AXC Resolution: 2.8→14 Å / SU B: 13.2 / SU ML: 0.25 / Cross valid method: THROUGHOUT / ESU R: 0.647 / ESU R Free: 0.338
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Displacement parameters | Biso mean: 54.299 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→14 Å
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