+Open data
-Basic information
Entry | Database: PDB / ID: 3v60 | ||||||
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Title | Structure of S. cerevisiae PCNA conjugated to SUMO on lysine 164 | ||||||
Components |
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Keywords | PROTEIN BINDING/DNA BINDING PROTEIN / UBIQUITIN-LIKE PROTEIN PCNA / POST-TRANSLATIONAL MODIFICATION DNA REPLICATION DNA DAMAGE RESPONSE / SRS2 / NUCLEAR / PROTEIN BINDING-DNA BINDING PROTEIN complex | ||||||
Function / homology | Function and homology information SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMO is proteolytically processed / SUMOylation of transcription factors / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of transcription cofactors / meiotic mismatch repair / Processive synthesis on the lagging strand ...SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMO is proteolytically processed / SUMOylation of transcription factors / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of transcription cofactors / meiotic mismatch repair / Processive synthesis on the lagging strand / Removal of the Flap Intermediate / SUMOylation of DNA damage response and repair proteins / E3 ubiquitin ligases ubiquitinate target proteins / Polymerase switching / SUMOylation of DNA replication proteins / positive regulation of DNA metabolic process / maintenance of DNA trinucleotide repeats / septin ring / Translesion Synthesis by POLH / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / establishment of mitotic sister chromatid cohesion / PCNA complex / SUMOylation of SUMOylation proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Termination of translesion DNA synthesis / lagging strand elongation / SUMOylation of RNA binding proteins / postreplication repair / SUMOylation of chromatin organization proteins / silent mating-type cassette heterochromatin formation / mitotic sister chromatid cohesion / error-free translesion synthesis / DNA polymerase processivity factor activity / leading strand elongation / ubiquitin-like protein ligase binding / protein sumoylation / Dual incision in TC-NER / subtelomeric heterochromatin formation / mismatch repair / translesion synthesis / positive regulation of DNA repair / condensed nuclear chromosome / replication fork / positive regulation of DNA replication / nucleotide-excision repair / PML body / protein tag activity / mitotic cell cycle / chromosome, telomeric region / DNA binding / identical protein binding / nucleus Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Armstrong, A.A. / Mohideen, F. / Lima, C.D. | ||||||
Citation | Journal: Nature / Year: 2012 Title: Recognition of SUMO-modified PCNA requires tandem receptor motifs in Srs2. Authors: Armstrong, A.A. / Mohideen, F. / Lima, C.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3v60.cif.gz | 82.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3v60.ent.gz | 63.2 KB | Display | PDB format |
PDBx/mmJSON format | 3v60.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3v60_validation.pdf.gz | 448.1 KB | Display | wwPDB validaton report |
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Full document | 3v60_full_validation.pdf.gz | 453.5 KB | Display | |
Data in XML | 3v60_validation.xml.gz | 15.4 KB | Display | |
Data in CIF | 3v60_validation.cif.gz | 21 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v6/3v60 ftp://data.pdbj.org/pub/pdb/validation_reports/v6/3v60 | HTTPS FTP |
-Related structure data
Related structure data | 3v61C 3v62C 1euvS 1plqS 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: 9719.982 Da / Num. of mol.: 1 / Fragment: unp resicues 20-98 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: W3031A / Gene: D9719.15, SMT3, YDR510W / Plasmid: PET28B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) PLYSS / References: UniProt: Q12306 | ||||
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#2: Protein | Mass: 28871.922 Da / Num. of mol.: 1 / Mutation: K127G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: W3031A / Gene: POL30, YBR0811, YBR088C / Plasmid: PET21B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CP RIL / References: UniProt: P15873 | ||||
#3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | Compound details | THERE IS AN ISOPEPTIDE | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 5.2 Å3/Da / Density % sol: 76.36 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 4% PEG 8000, 500 mM LiSO4, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 10, 2007 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.6→50 Å / Num. all: 314610 / Num. obs: 25873 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 12.2 % / Rmerge(I) obs: 0.052 / Χ2: 1.509 / Net I/σ(I): 21.7 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entries 1PLQ and 1EUV Resolution: 2.6→50 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.933 / Occupancy max: 1 / Occupancy min: 1 / SU B: 5.95 / SU ML: 0.125 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.255 / ESU R Free: 0.223 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: 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 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 155.18 Å2 / Biso mean: 62.2473 Å2 / Biso min: 36.04 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.668 Å / Total num. of bins used: 20
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