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Yorodumi- PDB-1ldk: Structure of the Cul1-Rbx1-Skp1-F boxSkp2 SCF Ubiquitin Ligase Complex -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ldk | ||||||
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Title | Structure of the Cul1-Rbx1-Skp1-F boxSkp2 SCF Ubiquitin Ligase Complex | ||||||
Components |
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Keywords | LIGASE / SCF / cullin / rbx1 / roc1 / hrt1 / skp1 / skp2 / F-box / fbox / ubiquitin / ubiquitination / E3 ligase | ||||||
Function / homology | Function and homology information positive regulation of protein polyubiquitination / Parkin-FBXW7-Cul1 ubiquitin ligase complex / F-box domain binding / Aberrant regulation of mitotic exit in cancer due to RB1 defects / PcG protein complex / cullin-RING-type E3 NEDD8 transferase / cellular response to chemical stress / NEDD8 transferase activity / cullin-RING ubiquitin ligase complex / Cul7-RING ubiquitin ligase complex ...positive regulation of protein polyubiquitination / Parkin-FBXW7-Cul1 ubiquitin ligase complex / F-box domain binding / Aberrant regulation of mitotic exit in cancer due to RB1 defects / PcG protein complex / cullin-RING-type E3 NEDD8 transferase / cellular response to chemical stress / NEDD8 transferase activity / cullin-RING ubiquitin ligase complex / Cul7-RING ubiquitin ligase complex / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / positive regulation of ubiquitin protein ligase activity / maintenance of protein location in nucleus / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / positive regulation of protein autoubiquitination / protein neddylation / NEDD8 ligase activity / Cul5-RING ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / ubiquitin-ubiquitin ligase activity / Cul4A-RING E3 ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex / SCF ubiquitin ligase complex / positive regulation of intracellular estrogen receptor signaling pathway / negative regulation of type I interferon production / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / Cul3-RING ubiquitin ligase complex / 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 / positive regulation of TORC1 signaling / Regulation of BACH1 activity / T cell activation / post-translational protein modification / MAP3K8 (TPL2)-dependent MAPK1/3 activation / intrinsic apoptotic signaling pathway / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / molecular function activator activity / Vpu mediated degradation of CD4 / Degradation of DVL / Recognition of DNA damage by PCNA-containing replication complex / Dectin-1 mediated noncanonical NF-kB signaling / cellular response to amino acid stimulus / 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 / animal organ morphogenesis / Vif-mediated degradation of APOBEC3G / Hedgehog 'on' state / DNA Damage Recognition in GG-NER / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / G1/S transition of mitotic cell cycle / negative regulation of canonical Wnt signaling pathway / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / RING-type E3 ubiquitin transferase / 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 / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / NOTCH1 Intracellular Domain Regulates Transcription / Formation of TC-NER Pre-Incision Complex / 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 / Formation of Incision Complex in GG-NER / Regulation of expression of SLITs and ROBOs / FCERI mediated NF-kB activation / Interleukin-1 signaling / Dual incision in TC-NER / protein polyubiquitination / Orc1 removal from chromatin / Gap-filling DNA repair synthesis and ligation in TC-NER / Regulation of RAS by GAPs / positive regulation of protein catabolic process / Regulation of RUNX2 expression and activity / cellular response to UV / Cyclin D associated events in G1 / ubiquitin protein ligase activity / KEAP1-NFE2L2 pathway / G2/M transition of mitotic cell cycle / Regulation of PLK1 Activity at G2/M Transition / MAPK cascade / protein-macromolecule adaptor activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / Circadian Clock / Downstream TCR signaling / Neddylation / ubiquitin-dependent protein catabolic process Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | ||||||
Authors | Zheng, N. / Schulman, B.A. / Song, L. / Miller, J.J. / Jeffrey, P.D. / Wang, P. / Chu, C. / Koepp, D.M. / Elledge, S.J. / Pagano, M. ...Zheng, N. / Schulman, B.A. / Song, L. / Miller, J.J. / Jeffrey, P.D. / Wang, P. / Chu, C. / Koepp, D.M. / Elledge, S.J. / Pagano, M. / Conaway, R.C. / Conaway, J.W. / Harper, J.W. / Pavletich, N.P. | ||||||
Citation | Journal: Nature / Year: 2002 Title: Structure of the Cul1-Rbx1-Skp1-F boxSkp2 SCF ubiquitin ligase complex. Authors: Zheng, N. / Schulman, B.A. / Song, L. / Miller, J.J. / Jeffrey, P.D. / Wang, P. / Chu, C. / Koepp, D.M. / Elledge, S.J. / Pagano, M. / Conaway, R.C. / Conaway, J.W. / Harper, J.W. / 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 | 1ldk.cif.gz | 209.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ldk.ent.gz | 170 KB | Display | PDB format |
PDBx/mmJSON format | 1ldk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ld/1ldk ftp://data.pdbj.org/pub/pdb/validation_reports/ld/1ldk | HTTPS FTP |
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-Related 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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-Components
-Protein , 4 types, 4 molecules ABCD
#1: Protein | Mass: 45754.766 Da / Num. of mol.: 1 / Fragment: RESIDUES 15-410 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX4T1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13616 |
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#2: Protein | Mass: 42507.910 Da / Num. of mol.: 1 / Fragment: RESIDUES 411-776 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX4T1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13616 |
#3: Protein | Mass: 10655.229 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX4T1 / Production host: Escherichia coli (E. coli) / References: UniProt: P62877 |
#4: Protein | Mass: 15033.173 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX4T1 / Production host: Escherichia coli (E. coli) / References: UniProt: P63208 |
-Protein/peptide / Non-polymers , 2 types, 4 molecules E
#5: Protein/peptide | Mass: 4759.569 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX4T1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13309 |
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#6: Chemical |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 5 |
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-Sample preparation
Crystal | Density Matthews: 3.7 Å3/Da / Density % sol: 66.77 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: peg4k, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector | Type: ADSC QUANTUM 4 / Detector: CCD | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 3.1→20 Å / Num. obs: 30847 / Observed criterion σ(I): 0 | |||||||||||||||
Reflection | *PLUS Lowest resolution: 20 Å / % possible obs: 88.8 % / Num. measured all: 123884 / Rmerge(I) obs: 0.091 | |||||||||||||||
Reflection shell | *PLUS % possible obs: 63.5 % / Rmerge(I) obs: 0.332 / Mean I/σ(I) obs: 2.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→20 Å / σ(F): 0 /
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Refinement step | Cycle: LAST / Resolution: 3.1→20 Å
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Refinement | *PLUS Highest resolution: 3.2 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor obs: 0.289 | |||||||||||||||
Solvent computation | *PLUS | |||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.513 / Rfactor Rwork: 0.473 |