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Yorodumi- PDB-3v62: Structure of the S. cerevisiae Srs2 C-terminal domain in complex ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3v62 | ||||||
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Title | Structure of the S. cerevisiae Srs2 C-terminal domain in complex with 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 / NEM MODIFICATION ON PCNA CYS22 AND CYS81 REDUCTIVE METHYLATION OF ALL LYSINE RESIDUES ON SMT3 / NUCLEAR / PROTEIN BINDING-DNA BINDING PROTEIN complex | ||||||
Function / homology | Function and homology information DNA recombinase disassembly / 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 ...DNA recombinase disassembly / 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 / SUMOylation of DNA damage response and repair proteins / Processive synthesis on the lagging strand / Removal of the Flap Intermediate / E3 ubiquitin ligases ubiquitinate target proteins / Translesion Synthesis by POLH / Polymerase switching / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / SUMOylation of DNA replication proteins / positive regulation of DNA metabolic process / maintenance of DNA trinucleotide repeats / septin ring / negative regulation of DNA recombination / PCNA complex / establishment of mitotic sister chromatid cohesion / Termination of translesion DNA synthesis / SUMOylation of SUMOylation proteins / DNA protection / positive regulation of endodeoxyribonuclease activity / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / SUMOylation of RNA binding proteins / lagging strand elongation / recombinational repair / postreplication repair / SUMOylation of chromatin organization proteins / silent mating-type cassette heterochromatin formation / DNA duplex unwinding / mitotic sister chromatid cohesion / 3'-5' DNA helicase activity / 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 / negative regulation of double-strand break repair via homologous recombination / mismatch repair / translesion synthesis / enzyme activator activity / positive regulation of DNA repair / replication fork / condensed nuclear chromosome / positive regulation of DNA replication / nucleotide-excision repair / PML body / double-strand break repair via nonhomologous end joining / protein tag activity / mitotic cell cycle / DNA helicase / chromosome, telomeric region / DNA repair / DNA binding / ATP binding / identical protein binding / nucleus Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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 | 3v62.cif.gz | 158.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3v62.ent.gz | 124.2 KB | Display | PDB format |
PDBx/mmJSON format | 3v62.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v6/3v62 ftp://data.pdbj.org/pub/pdb/validation_reports/v6/3v62 | HTTPS FTP |
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-Related structure data
Related structure data | 3v60C 3v61C 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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Details | PCNA IS NORMALLY A TRIMER BUT NEM MODIFICATION DISRUPTS THE TRIMER AND CAUSES PCNA TO RUN AS A MONOMER ON GEL FILTRATION THIS SUMO-PCNA MONOMER CRYSTALLIZES BY REFORMING THE PCNA:PCNA PROTOMER BUT WITH A RIGHT HANDED HELICAL SCREW COMPOSED OF 4 SUBUNITS THE ASU HAS 2 AND THE UNIT CELL CONTAINS ONE TURN OF THIS HELICAL SCREW WITH 4 PROTOMERS |
-Components
-Protein , 3 types, 6 molecules ADBECF
#1: Protein | Mass: 9882.258 Da / Num. of mol.: 2 / Fragment: unp residues 20-98 / Mutation: GSH from N-tag after thrombin cleavage, K19R 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 #2: Protein | Mass: 28871.922 Da / Num. of mol.: 2 / 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: Protein | Mass: 7703.804 Da / Num. of mol.: 2 / Fragment: unp residues 1107-1174 / Mutation: S at N-terminal after Ulp1 cleavage Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: W3031A / Gene: HPR5, J0913, RADH, SRS2, YJL092W / Plasmid: PSMT3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CP RIL / References: UniProt: P12954, DNA helicase |
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-Non-polymers , 3 types, 59 molecules
#4: Chemical | ChemComp-NEQ / #5: Chemical | ChemComp-SO4 / #6: Water | ChemComp-HOH / | |
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-Details
Compound details | THERE IS AN ISOPEPTIDE |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.26 Å3/Da / Density % sol: 62.21 % |
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Crystal grow | Temperature: 279 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.9 M AMMONIUM SULFATE 4% PEG 400 100 mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 279K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 20, 2010 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.9→50 Å / Num. all: 101080 / Num. obs: 26583 / % possible obs: 99.7 % / Observed criterion σ(I): -1 / Redundancy: 3.8 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 11.8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 2.9→50 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.938 / Occupancy max: 1 / Occupancy min: 1 / SU B: 15.141 / SU ML: 0.274 / Cross valid method: THROUGHOUT / ESU R: 0.862 / ESU R Free: 0.334 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: NEM molecule has occupancy of 1 as mass spec suggested that this ligand is fully modified in the studied samples.
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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 mean: 88.556 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→50 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.899→2.975 Å / Total num. of bins used: 20
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