+Open data
-Basic information
Entry | Database: PDB / ID: 5an3 | ||||||
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Title | Structure of an Sgt1-Skp1 Complex | ||||||
Components |
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Keywords | TRANSCRIPTION | ||||||
Function / homology | Function and homology information protein-containing complex assembly => GO:0065003 / 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 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / septin ring assembly ...protein-containing complex assembly => GO:0065003 / 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 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / septin ring assembly / regulation of exit from mitosis / Antigen processing: Ubiquitination & Proteasome degradation / vacuolar acidification / kinetochore assembly / regulation of metabolic process / exit from mitosis / positive regulation of glucose transmembrane transport / protein neddylation / mitotic intra-S DNA damage checkpoint signaling / mitochondrial fusion / silent mating-type cassette heterochromatin formation / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / SCF ubiquitin ligase complex / DNA replication origin binding / cullin family protein binding / subtelomeric heterochromatin formation / cAMP-mediated signaling / regulation of protein-containing complex assembly / endomembrane system / negative regulation of cytoplasmic translation / ubiquitin ligase complex / regulation of mitotic cell cycle / G1/S transition of mitotic cell cycle / regulation of protein stability / kinetochore / G2/M transition of mitotic cell cycle / protein-macromolecule adaptor activity / mitotic cell cycle / ubiquitin-dependent protein catabolic process / protein-folding chaperone binding / protein-containing complex assembly / chromosome, telomeric region / protein stabilization / protein ubiquitination / cell cycle / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | SACCHAROMYCES CEREVISIAE (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.82 Å | ||||||
Authors | Willhoft, O. / Vaughan, C.K. | ||||||
Citation | Journal: Sci Rep / Year: 2017 Title: The crystal structure of the Sgt1-Skp1 complex: the link between Hsp90 and both SCF E3 ubiquitin ligases and kinetochores. Authors: Willhoft, O. / Kerr, R. / Patel, D. / Zhang, W. / Al-Jassar, C. / Daviter, T. / Millson, S.H. / Thalassinos, K. / Vaughan, C.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5an3.cif.gz | 200.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5an3.ent.gz | 161.5 KB | Display | PDB format |
PDBx/mmJSON format | 5an3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/an/5an3 ftp://data.pdbj.org/pub/pdb/validation_reports/an/5an3 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 17492.070 Da / Num. of mol.: 3 / Fragment: TPR DOMAIN, UNP RESIDUES 1-150 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): T7 EXPRESS LYSY/IQ / References: UniProt: Q08446 #2: Protein | | Mass: 14886.524 Da / Num. of mol.: 1 / Fragment: BTBPOZ DOMAIN, UNP RESIDUES 1-35,65-158 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): T7 EXPRESS LYSY/IQ / References: UniProt: P52286 #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.84 % / Description: NONE |
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Crystal grow | Details: 0.325 M MGCL2, 22.5% PEG-6000, 0.1 M TRIS-HCL PH 8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.979494 |
Detector | Type: ADSC ADSC Q105 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979494 Å / Relative weight: 1 |
Reflection | Resolution: 2.82→81.89 Å / Num. obs: 15826 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 21.5 % / Biso Wilson estimate: 86.92 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 29.2 |
Reflection shell | Resolution: 2.82→2.89 Å / Redundancy: 21.9 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 4.9 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 2.82→19.88 Å / Cor.coef. Fo:Fc: 0.9337 / Cor.coef. Fo:Fc free: 0.8998 / SU R Cruickshank DPI: 1.211 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.105 / SU Rfree Blow DPI: 0.322 / SU Rfree Cruickshank DPI: 0.33 Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
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Displacement parameters | Biso mean: 70.85 Å2
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Refine analyze | Luzzati coordinate error obs: 0.441 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.82→19.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.82→3.02 Å / Total num. of bins used: 8
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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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