+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3317 | |||||||||
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Title | Negative stain EM structure of CSN-N8-CRL3 at 27 A resolution | |||||||||
Map data | Negative stain reconstruction of CSN-N8-CRL3 | |||||||||
Sample |
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Keywords | COP9 Signalosome / Cullin-RING ligases / Cryo-EM | |||||||||
Function / homology | Function and homology information Prolactin receptor signaling / regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / COP9 signalosome assembly / Regulation of BACH1 activity / Recognition of DNA damage by PCNA-containing replication complex / DNA Damage Recognition in GG-NER / Formation of TC-NER Pre-Incision Complex / trophectodermal cell proliferation / Dual Incision in GG-NER / macrophage migration inhibitory factor binding ...Prolactin receptor signaling / regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / COP9 signalosome assembly / Regulation of BACH1 activity / Recognition of DNA damage by PCNA-containing replication complex / DNA Damage Recognition in GG-NER / Formation of TC-NER Pre-Incision Complex / trophectodermal cell proliferation / Dual Incision in GG-NER / macrophage migration inhibitory factor binding / Dual incision in TC-NER / Formation of Incision Complex in GG-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / liver morphogenesis / positive regulation of mitotic cell cycle phase transition / trophectodermal cellular morphogenesis / POZ domain binding / Regulation of RAS by GAPs / Regulation of RUNX2 expression and activity / Degradation of GLI1 by the proteasome / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Degradation of DVL / Orc1 removal from chromatin / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / regulation of IRE1-mediated unfolded protein response / Hedgehog 'on' state / Degradation of beta-catenin by the destruction complex / exosomal secretion / nuclear protein quality control by the ubiquitin-proteasome system / eukaryotic initiation factor 4E binding / deNEDDylase activity / GTPase inhibitor activity / regulation protein catabolic process at postsynapse / Interleukin-1 signaling / polar microtubule / eukaryotic translation initiation factor 3 complex / regulation of protein neddylation / protein deneddylation / anaphase-promoting complex / KEAP1-NFE2L2 pathway / COPII vesicle coating / GLI3 is processed to GLI3R by the proteasome / anaphase-promoting complex-dependent catabolic process / positive regulation of mitotic metaphase/anaphase transition / cullin-RING-type E3 NEDD8 transferase / stem cell division / Neddylation / RHOBTB3 ATPase cycle / Antigen processing: Ubiquitination & Proteasome degradation / cullin-RING ubiquitin ligase complex / embryonic cleavage / cell projection organization / COP9 signalosome / Cul7-RING ubiquitin ligase complex / metal-dependent deubiquitinase activity / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / regulation of proteolysis / activation of NF-kappaB-inducing kinase activity / VCB complex / positive regulation of protein autoubiquitination / protein neddylation / Hydrolases; Acting on peptide bonds (peptidases) / Notch binding / NEDD8 ligase activity / Cul5-RING ubiquitin ligase complex / RHOBTB1 GTPase cycle / fibroblast apoptotic process / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / ubiquitin-ubiquitin ligase activity / Cul4A-RING E3 ubiquitin ligase complex / negative regulation of Rho protein signal transduction / Cul2-RING ubiquitin ligase complex / SCF ubiquitin ligase complex / inner cell mass cell proliferation / negative regulation of type I interferon production / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / mitotic metaphase chromosome alignment / Cul3-RING ubiquitin ligase complex / molecular function inhibitor activity / stress fiber assembly / protein deubiquitination / positive regulation of cytokinesis / skeletal muscle cell differentiation / protein monoubiquitination / TGF-beta receptor signaling activates SMADs / cullin family protein binding / regulation of JNK cascade / response to light stimulus / gastrulation / anatomical structure morphogenesis / protein K48-linked ubiquitination / sperm flagellum / endoplasmic reticulum to Golgi vesicle-mediated transport / localization / protein autoubiquitination / RHOBTB2 GTPase cycle / ubiquitin ligase complex / JNK cascade Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 27.0 Å | |||||||||
Authors | Cavadini S / Fischer ES / Bunker RD / Potenza A / Lingaraju GM / Goldie KN / Mohamed WI / Faty M / Petzold G / Beckwith REJ ...Cavadini S / Fischer ES / Bunker RD / Potenza A / Lingaraju GM / Goldie KN / Mohamed WI / Faty M / Petzold G / Beckwith REJ / Tichkule R / Hassiepen U / Abdulrahman W / Pantelic RS / Matsumoto S / Sugasawa K / Stahlberg H / Thoma NH | |||||||||
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
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_3317.map.gz | 7.5 MB | EMDB map data format | |
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Header (meta data) | emd-3317-v30.xml emd-3317.xml | 18.6 KB 18.6 KB | Display Display | EMDB header |
Images | emd_3317.png | 499.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3317 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3317 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_3317.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Negative stain reconstruction of CSN-N8-CRL3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 4.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
+Entire : Recombinant human CSN-N8-CRL3 complex
+Supramolecule #1000: Recombinant human CSN-N8-CRL3 complex
+Macromolecule #1: COP9 signalosome subunit 1
+Macromolecule #2: COP9 signalosome subunit 2
+Macromolecule #3: COP9 signalosome subunit 3
+Macromolecule #4: COP9 signalosome subunit 4
+Macromolecule #5: COP9 signalosome subunit 5
+Macromolecule #6: COP9 signalosome subunit 6
+Macromolecule #7: COP9 signalosome subunit 7A
+Macromolecule #8: COP9 signalosome subunit 8
+Macromolecule #9: CUL3
+Macromolecule #10: Speckle-type POZ protein
+Macromolecule #11: E3 UBIQUITIN-PROTEIN LIGASE RBX1
+Macromolecule #12: NEDD8
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.1 mg/mL |
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Buffer | pH: 7.4 / Details: 50mM HEPES, 200mM NaCl, 0.25mM TCEP |
Staining | Type: NEGATIVE Details: Samples were applied to the grids and, after blotting, negatively stained with 2% (w/v) uranyl acetate. |
Grid | Details: Quantifoil grids (S7/2, Cu 400 mesh) with thin carbon. |
Vitrification | Cryogen name: NONE / Instrument: OTHER |
-Electron microscopy
Microscope | FEI/PHILIPS CM200FEG |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm |
Sample stage | Specimen holder model: GATAN LIQUID NITROGEN |
Date | Sep 1, 2013 |
Image recording | Category: CCD / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) |
-Image processing
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 27.0 Å / Resolution method: OTHER / Software - Name: EMAN2, SPARX, RELION / Number images used: 33749 |
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-Atomic model buiding 1
Initial model | PDB ID: |
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Refinement | Space: REAL / Protocol: RIGID BODY FIT |
-Atomic model buiding 2
Initial model | PDB ID: |
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Refinement | Space: REAL / Protocol: RIGID BODY FIT |