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Open data
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Basic information
| Entry | Database: PDB / ID: 4wsn | ||||||
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| Title | Crystal structure of the COP9 signalosome, a P1 crystal form | ||||||
Components | (COP9 signalosome complex subunit ...) x 8 | ||||||
Keywords | SIGNALING PROTEIN / hydrolase | ||||||
| Function / homology | Function and homology informationCOP9 signalosome assembly / macrophage migration inhibitory factor binding / regulation of IRE1-mediated unfolded protein response / exosomal secretion / GTPase inhibitor activity / deNEDDylase activity / activation of NF-kappaB-inducing kinase activity / protein deneddylation / regulation of protein neddylation / eukaryotic translation initiation factor 3 complex ...COP9 signalosome assembly / macrophage migration inhibitory factor binding / regulation of IRE1-mediated unfolded protein response / exosomal secretion / GTPase inhibitor activity / deNEDDylase activity / activation of NF-kappaB-inducing kinase activity / protein deneddylation / regulation of protein neddylation / eukaryotic translation initiation factor 3 complex / COP9 signalosome / deubiquitinase activity / protein neddylation / Hydrolases; Acting on peptide bonds (peptidases) / regulation of JNK cascade / regulation of DNA damage response, signal transduction by p53 class mediator / RHOBTB1 GTPase cycle / metal-dependent deubiquitinase activity / intercellular bridge / response to light stimulus / JNK cascade / GSK3B-mediated proteasomal degradation of PD-L1(CD274) / translation initiation factor activity / post-translational protein modification / DNA Damage Recognition in GG-NER / neuron differentiation / Formation of TC-NER Pre-Incision Complex / metallopeptidase activity / transcription corepressor activity / transcription by RNA polymerase II / Cargo recognition for clathrin-mediated endocytosis / synaptic vesicle / Neddylation / ubiquitin-dependent protein catabolic process / protein phosphorylation / transcription coactivator activity / regulation of cell cycle / nuclear speck / translation / negative regulation of cell population proliferation / negative regulation of apoptotic process / chromatin / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / enzyme binding / signal transduction / positive regulation of transcription by RNA polymerase II / proteolysis / extracellular exosome / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
| Biological species | Homo sapiens (human) | ||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 5.5 Å | ||||||
Authors | Bunker, R.D. / Lingaraju, G.M. / Thoma, N.H. | ||||||
Citation | Journal: Nature / Year: 2016Title: Cullin-RING ubiquitin E3 ligase regulation by the COP9 signalosome. Authors: Simone Cavadini / Eric S Fischer / Richard D Bunker / Alessandro Potenza / Gondichatnahalli M Lingaraju / Kenneth N Goldie / Weaam I Mohamed / Mahamadou Faty / Georg Petzold / Rohan E J ...Authors: Simone Cavadini / Eric S Fischer / Richard D Bunker / Alessandro Potenza / Gondichatnahalli M Lingaraju / Kenneth N Goldie / Weaam I Mohamed / Mahamadou Faty / Georg Petzold / Rohan E J Beckwith / Ritesh B Tichkule / Ulrich Hassiepen / Wassim Abdulrahman / Radosav S Pantelic / Syota Matsumoto / Kaoru Sugasawa / Henning Stahlberg / Nicolas H Thomä / ![]() Abstract: The cullin-RING ubiquitin E3 ligase (CRL) family comprises over 200 members in humans. The COP9 signalosome complex (CSN) regulates CRLs by removing their ubiquitin-like activator NEDD8. The CUL4A- ...The cullin-RING ubiquitin E3 ligase (CRL) family comprises over 200 members in humans. The COP9 signalosome complex (CSN) regulates CRLs by removing their ubiquitin-like activator NEDD8. The CUL4A-RBX1-DDB1-DDB2 complex (CRL4A(DDB2)) monitors the genome for ultraviolet-light-induced DNA damage. CRL4A(DBB2) is inactive in the absence of damaged DNA and requires CSN to regulate the repair process. The structural basis of CSN binding to CRL4A(DDB2) and the principles of CSN activation are poorly understood. Here we present cryo-electron microscopy structures for CSN in complex with neddylated CRL4A ligases to 6.4 Å resolution. The CSN conformers defined by cryo-electron microscopy and a novel apo-CSN crystal structure indicate an induced-fit mechanism that drives CSN activation by neddylated CRLs. We find that CSN and a substrate cannot bind simultaneously to CRL4A, favouring a deneddylated, inactive state for substrate-free CRL4 complexes. These architectural and regulatory principles appear conserved across CRL families, allowing global regulation by CSN. | ||||||
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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| PDBx/mmCIF format | 4wsn.cif.gz | 6.1 MB | Display | PDBx/mmCIF format |
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| PDB format | pdb4wsn.ent.gz | Display | PDB format | |
| PDBx/mmJSON format | 4wsn.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ws/4wsn ftp://data.pdbj.org/pub/pdb/validation_reports/ws/4wsn | HTTPS FTP |
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-Related structure data
| Related structure data | ![]() 3313C ![]() 3314C ![]() 3315C ![]() 3316C ![]() 3317C ![]() 4d10S S: Starting model for refinement C: citing same article ( |
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Assembly
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| Noncrystallographic symmetry (NCS) | NCS domain:
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About Yorodumi




Homo sapiens (human)
X-RAY DIFFRACTION
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