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- PDB-3l10: Structure of split monoubiquitinated PCNA with ubiquitin in posit... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3l10 | ||||||
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Title | Structure of split monoubiquitinated PCNA with ubiquitin in position one | ||||||
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![]() | REPLICATION / DNA damage / DNA repair / DNA replication / DNA-binding / Isopeptide bond / Nucleus / Ubl conjugation | ||||||
Function / homology | ![]() : / : / : / : / : / Regulation of TP53 Degradation / Regulation of PTEN localization / ER Quality Control Compartment (ERQC) / UCH proteinases / Interleukin-1 signaling ...: / : / : / : / : / Regulation of TP53 Degradation / Regulation of PTEN localization / ER Quality Control Compartment (ERQC) / UCH proteinases / Interleukin-1 signaling / Aggrephagy / Peroxisomal protein import / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / ABC-family proteins mediated transport / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / meiotic mismatch repair / Metalloprotease DUBs / Endosomal Sorting Complex Required For Transport (ESCRT) / Processive synthesis on the lagging strand / Removal of the Flap Intermediate / E3 ubiquitin ligases ubiquitinate target proteins / Polymerase switching / SUMOylation of DNA replication proteins / positive regulation of DNA metabolic process / maintenance of DNA trinucleotide repeats / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / Translesion Synthesis by POLH / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / establishment of mitotic sister chromatid cohesion / PCNA complex / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Termination of translesion DNA synthesis / Negative regulators of DDX58/IFIH1 signaling / lagging strand elongation / postreplication repair / silent mating-type cassette heterochromatin formation / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / mitotic sister chromatid cohesion / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / error-free translesion synthesis / Regulation of PTEN stability and activity / DNA polymerase processivity factor activity / CDK-mediated phosphorylation and removal of Cdc6 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Formation of TC-NER Pre-Incision Complex / Major pathway of rRNA processing in the nucleolus and cytosol / leading strand elongation / Orc1 removal from chromatin / MAPK6/MAPK4 signaling / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Gap-filling DNA repair synthesis and ligation in TC-NER / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Antigen processing: Ubiquitination & Proteasome degradation / L13a-mediated translational silencing of Ceruloplasmin expression / Dual incision in TC-NER / ribosomal large subunit export from nucleus / subtelomeric heterochromatin formation / Ub-specific processing proteases / mismatch repair / translesion synthesis / positive regulation of DNA repair / replication fork / positive regulation of DNA replication / nucleotide-excision repair / ribosomal large subunit assembly / modification-dependent protein catabolic process / protein tag activity / ribosome biogenesis / mitotic cell cycle / ribosomal small subunit assembly / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / chromosome, telomeric region / cytoplasmic translation / protein ubiquitination / structural constituent of ribosome / ubiquitin protein ligase binding / DNA binding / identical protein binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Freudenthal, B.D. / Gakhar, L. / Ramaswamy, S. / Washington, M.T. | ||||||
![]() | ![]() Title: Structure of monoubiquitinated PCNA and implications for translesion synthesis and DNA polymerase exchange. Authors: Freudenthal, B.D. / Gakhar, L. / Ramaswamy, S. / Washington, M.T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 75.9 KB | Display | ![]() |
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PDB format | ![]() | 57 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 434 KB | Display | ![]() |
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Full document | ![]() | 456.3 KB | Display | |
Data in XML | ![]() | 16.2 KB | Display | |
Data in CIF | ![]() | 20.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3l0wC ![]() 3l0xC ![]() 1plqS C: citing same article ( S: Starting model for refinement |
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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: 19238.893 Da / Num. of mol.: 1 / Fragment: N fragment Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: POL30, YBR0811, YBR088C / Plasmid: petduet-1 / Production host: ![]() ![]() |
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#2: Protein | Mass: 18714.408 Da / Num. of mol.: 1 / Fragment: Ubi-C fragment Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: POL30, Pol30 & UBI1, YBR0811, YBR088C / Plasmid: petduet-1 / Production host: ![]() ![]() References: UniProt: P61864, UniProt: P15873, UniProt: P05759*PLUS |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.04 Å3/Da / Density % sol: 69.54 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: 2.04M ammonium sulfate, 0.1M sodium citrate, 3% ethanol, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: NOIR-1 / Detector: CCD / Date: Mar 25, 2009 / Details: saggitally focused mirrors |
Radiation | Monochromator: Saggitally focused mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→86.63 Å / Num. obs: 15333 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 8.74 % / Biso Wilson estimate: 88.237 Å2 / Rmerge(I) obs: 0.109 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 5.38 % / Rmerge(I) obs: 0.604 / Mean I/σ(I) obs: 2.4 / Num. unique all: 1471 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 1PLQ Resolution: 2.8→86 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.875 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 18.201 / SU ML: 0.365 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R: 1.084 / ESU R Free: 0.421 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 125.95 Å2 / Biso mean: 86.057 Å2 / Biso min: 20 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→86 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.873 Å / Total num. of bins used: 20
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