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Yorodumi- PDB-3mks: Crystal Structure of yeast Cdc4/Skp1 in complex with an allosteri... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3mks | ||||||
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Title | Crystal Structure of yeast Cdc4/Skp1 in complex with an allosteric inhibitor SCF-I2 | ||||||
Components |
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Keywords | LIGASE/CELL CYCLE / ubiquitin ligase / protein binding / small molecule complex / LIGASE-CELL CYCLE complex | ||||||
Function / homology | Function and homology information RAVE complex / Iron uptake and transport / CBF3 complex / regulation of transcription by galactose / regulation of sulfur amino acid metabolic process / cellular response to methylmercury / vacuolar proton-transporting V-type ATPase complex assembly / septin ring assembly / nuclear SCF ubiquitin ligase complex / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) ...RAVE complex / Iron uptake and transport / CBF3 complex / regulation of transcription by galactose / regulation of sulfur amino acid metabolic process / cellular response to methylmercury / vacuolar proton-transporting V-type ATPase complex assembly / septin ring assembly / nuclear SCF ubiquitin ligase complex / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / regulation of exit from mitosis / kinetochore assembly / vacuolar acidification / positive regulation of D-glucose transmembrane transport / protein neddylation / regulation of metabolic process / mitotic intra-S DNA damage checkpoint signaling / U3 snoRNA binding / silent mating-type cassette heterochromatin formation / mitochondrial fusion / exit from mitosis / SCF ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / sporulation resulting in formation of a cellular spore / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Orc1 removal from chromatin / DNA replication origin binding / cullin family protein binding / Antigen processing: Ubiquitination & Proteasome degradation / phosphoserine residue binding / 90S preribosome / regulation of protein-containing complex assembly / subtelomeric heterochromatin formation / endomembrane system / negative regulation of cytoplasmic translation / regulation of mitotic cell cycle / ubiquitin binding / meiotic cell cycle / kinetochore / nuclear matrix / G1/S transition of mitotic cell cycle / G2/M transition of mitotic cell cycle / mitotic cell cycle / ubiquitin-dependent protein catabolic process / protein-containing complex assembly / chromosome, telomeric region / protein ubiquitination / cell division / nucleolus / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å | ||||||
Authors | Orlicky, S. / Sicheri, F. / Tyers, M. / Tang, X. | ||||||
Citation | Journal: Nat.Biotechnol. / Year: 2010 Title: An allosteric inhibitor of substrate recognition by the SCF(Cdc4) ubiquitin ligase. Authors: Orlicky, S. / Tang, X. / Neduva, V. / Elowe, N. / Brown, E.D. / Sicheri, F. / Tyers, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3mks.cif.gz | 477.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mks.ent.gz | 395.3 KB | Display | PDB format |
PDBx/mmJSON format | 3mks.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3mks_validation.pdf.gz | 942.8 KB | Display | wwPDB validaton report |
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Full document | 3mks_full_validation.pdf.gz | 978.6 KB | Display | |
Data in XML | 3mks_validation.xml.gz | 44.3 KB | Display | |
Data in CIF | 3mks_validation.cif.gz | 61.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mk/3mks ftp://data.pdbj.org/pub/pdb/validation_reports/mk/3mks | HTTPS FTP |
-Related structure data
Related structure data | 1nexS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
-Protein , 2 types, 4 molecules ACBD
#1: Protein | Mass: 19504.561 Da / Num. of mol.: 2 / Fragment: UNP Residues 2-194 with 37-64 deleted Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: SKP1, CBF3D, YDR328C, D9798.14 / Plasmid: pProEx / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)codon plus / References: UniProt: P52286 #2: Protein | Mass: 52862.098 Da / Num. of mol.: 2 Fragment: UNP Residues 263-744 with 602-605 and 609-624 deleted Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: CDC4, YFL009W / Plasmid: pProEx / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)codon plus / References: UniProt: P07834 |
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-Non-polymers , 4 types, 53 molecules
#3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-C1C / | #5: Chemical | ChemComp-GOL / | #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | THE UNIPROT ENTRY FOR CDC4_YEAST INDICATES THAT K460E EXISTS AS A CONFLICT AND IS PRESENT IN THIS ENTRY |
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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: 3.87 Å3/Da / Density % sol: 68.24 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 1.5 M Ammonium sulfate, 100mM Tris pH 8.5, 15% glycerol, 1mM SCF-I2, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 12, 2004 Details: Si(111) double crystal monochromator, Bent cylindrical Si mirror (Rh coating) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Number: 374289 / Rmerge(I) obs: 0.058 / Χ2: 0.99 / D res high: 2.6 Å / D res low: 30 Å / Num. obs: 66680 / % possible obs: 99.8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 2.6→93.66 Å / Num. all: 66846 / Num. obs: 66846 / % possible obs: 99.8 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 24.3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Resolution: 2.6→2.688 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.435 / Mean I/σ(I) obs: 3.6 / % possible all: 100 |
-Phasing
Phasing | Method: molecular replacement |
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Phasing MR | Method rotation: fast direct / Method translation: &STRIP%trans_method |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1NEX Resolution: 2.6→93.66 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.894 / SU B: 21.478 / SU ML: 0.214 / Cross valid method: THROUGHOUT / ESU R: 0.34 / ESU R Free: 0.273 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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 mean: 54.854 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→93.66 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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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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