+Open data
-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 information regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / COP9 signalosome assembly / trophectodermal cell proliferation / macrophage migration inhibitory factor binding / regulation of IRE1-mediated unfolded protein response / exosomal secretion / deNEDDylase activity / GTPase inhibitor activity / eukaryotic translation initiation factor 3 complex / regulation of protein neddylation ...regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / COP9 signalosome assembly / trophectodermal cell proliferation / macrophage migration inhibitory factor binding / regulation of IRE1-mediated unfolded protein response / exosomal secretion / deNEDDylase activity / GTPase inhibitor activity / eukaryotic translation initiation factor 3 complex / regulation of protein neddylation / protein deneddylation / COP9 signalosome / metal-dependent deubiquitinase activity / activation of NF-kappaB-inducing kinase activity / protein neddylation / Hydrolases; Acting on peptide bonds (peptidases) / RHOBTB1 GTPase cycle / inner cell mass cell proliferation / protein deubiquitination / skeletal muscle cell differentiation / regulation of JNK cascade / response to light stimulus / JNK cascade / translation initiation factor activity / post-translational protein modification / DNA Damage Recognition in GG-NER / neuron differentiation / Formation of TC-NER Pre-Incision Complex / transcription corepressor activity / metallopeptidase activity / positive regulation of DNA-binding transcription factor activity / synaptic vesicle / Cargo recognition for clathrin-mediated endocytosis / cell junction / Neddylation / ubiquitin-dependent protein catabolic process / in utero embryonic development / transcription by RNA polymerase II / transcription coactivator activity / regulation of cell cycle / nuclear speck / translation / negative regulation of cell population proliferation / protein phosphorylation / chromatin / negative regulation of apoptotic process / 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: 2016 Title: 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
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 (ref.) |
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Similar structure data |
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-Assembly
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Noncrystallographic symmetry (NCS) | NCS domain:
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