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Yorodumi- PDB-1fs2: INSIGHTS INTO SCF UBIQUITIN LIGASES FROM THE STRUCTURE OF THE SKP... -
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-Basic information
Entry | Database: PDB / ID: 1fs2 | ||||||
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Title | INSIGHTS INTO SCF UBIQUITIN LIGASES FROM THE STRUCTURE OF THE SKP1-SKP2 COMPLEX | ||||||
Components |
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Keywords | LIGASE / Skp1 / Skp2 / F-box / LRRs / leucine-rich repeats / SCF / ubiquitin / E3 / ubiquitin protein ligase | ||||||
Function / homology | Function and homology information positive regulation of protein polyubiquitination / F-box domain binding / Aberrant regulation of mitotic exit in cancer due to RB1 defects / PcG protein complex / Cul7-RING ubiquitin ligase complex / positive regulation of ubiquitin protein ligase activity / maintenance of protein location in nucleus / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / SCF ubiquitin ligase complex ...positive regulation of protein polyubiquitination / F-box domain binding / Aberrant regulation of mitotic exit in cancer due to RB1 defects / PcG protein complex / Cul7-RING ubiquitin ligase complex / positive regulation of ubiquitin protein ligase activity / maintenance of protein location in nucleus / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / SCF ubiquitin ligase complex / positive regulation of intracellular estrogen receptor signaling pathway / ubiquitin ligase complex scaffold activity / Prolactin receptor signaling / protein monoubiquitination / cullin family protein binding / ubiquitin-like ligase-substrate adaptor activity / protein K48-linked ubiquitination / Nuclear events stimulated by ALK signaling in cancer / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / molecular function activator activity / Vpu mediated degradation of CD4 / Dectin-1 mediated noncanonical NF-kB signaling / Degradation of GLI1 by the proteasome / Activation of NF-kappaB in B cells / Negative regulation of NOTCH4 signaling / Iron uptake and transport / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / G1/S transition of mitotic cell cycle / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Degradation of beta-catenin by the destruction complex / NOTCH1 Intracellular Domain Regulates Transcription / CLEC7A (Dectin-1) signaling / SCF(Skp2)-mediated degradation of p27/p21 / beta-catenin binding / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / FCERI mediated NF-kB activation / Interleukin-1 signaling / protein polyubiquitination / Orc1 removal from chromatin / Regulation of RUNX2 expression and activity / Cyclin D associated events in G1 / G2/M transition of mitotic cell cycle / Regulation of PLK1 Activity at G2/M Transition / Antigen processing: Ubiquitination & Proteasome degradation / Circadian Clock / Downstream TCR signaling / Neddylation / proteasome-mediated ubiquitin-dependent protein catabolic process / regulation of apoptotic process / defense response to virus / protein ubiquitination / regulation of cell cycle / Ub-specific processing proteases / chromatin remodeling / protein domain specific binding / innate immune response / centrosome / nucleolus / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.9 Å | ||||||
Authors | Schulman, B.A. / Carrano, A.C. / Jeffrey, P.D. / Bowen, Z. / Kinnucan, E.R.E. / Finnin, M.S. / Elledge, S.J. / Harper, J.W. / Pagano, M. / Pavletich, N.P. | ||||||
Citation | Journal: Nature / Year: 2000 Title: Insights into SCF ubiquitin ligases from the structure of the Skp1-Skp2 complex. Authors: Schulman, B.A. / Carrano, A.C. / Jeffrey, P.D. / Bowen, Z. / Kinnucan, E.R. / Finnin, M.S. / Elledge, S.J. / Harper, J.W. / Pagano, M. / Pavletich, N.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1fs2.cif.gz | 156.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fs2.ent.gz | 124.9 KB | Display | PDB format |
PDBx/mmJSON format | 1fs2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fs/1fs2 ftp://data.pdbj.org/pub/pdb/validation_reports/fs/1fs2 | HTTPS FTP |
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-Related 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: 30771.318 Da / Num. of mol.: 2 / Fragment: RESIDUES 101-153; 193-410 (F-BOX + 8 LRRS) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q13309 #2: Protein | Mass: 16013.290 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-37; 43-147 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P63208 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.01 Å3/Da / Density % sol: 59.15 % | ||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.4 / Method: vapor diffusion, hanging drop / Details: microseeding | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2.9 Å / Num. obs: 23509 / % possible obs: 96.9 % / Num. measured all: 178486 / Rmerge(I) obs: 0.085 |
Reflection shell | *PLUS % possible obs: 98.7 % / Rmerge(I) obs: 0.388 / Mean I/σ(I) obs: 1.9 |
-Processing
Software |
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Refinement | Resolution: 2.9→20 Å / Rfactor Rfree: 0.287 / Rfactor Rwork: 0.246 / σ(F): 0 | ||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→20 Å
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.389 / Rfactor Rwork: 0.378 |