+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3315 | |||||||||
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Title | Cryo-EM structure of CSN-N8-CRL4A at 8.8 A resolution | |||||||||
Map data | Cryo-EM structure of CSN-N8-CRL4A at 8.8 A resolution | |||||||||
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 / Dual incision in TC-NER ...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 / Dual incision in TC-NER / Formation of Incision Complex in GG-NER / macrophage migration inhibitory factor binding / Gap-filling DNA repair synthesis and ligation in TC-NER / 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 / regulation of IRE1-mediated unfolded protein response / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Hedgehog 'on' state / negative regulation of granulocyte differentiation / Degradation of beta-catenin by the destruction complex / exosomal secretion / eukaryotic initiation factor 4E binding / deNEDDylase activity / GTPase inhibitor activity / Interleukin-1 signaling / regulation of protein neddylation / protein deneddylation / KEAP1-NFE2L2 pathway / anaphase-promoting complex / eukaryotic translation initiation factor 3 complex / activation of NF-kappaB-inducing kinase activity / GLI3 is processed to GLI3R by the proteasome / cullin-RING-type E3 NEDD8 transferase / Neddylation / cullin-RING ubiquitin ligase complex / Antigen processing: Ubiquitination & Proteasome degradation / regulation of DNA damage checkpoint / COP9 signalosome / positive regulation by virus of viral protein levels in host cell / Cul7-RING ubiquitin ligase complex / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / regulation of nucleotide-excision repair / epigenetic programming in the zygotic pronuclei / spindle assembly involved in female meiosis / regulation of proteolysis / VCB complex / positive regulation of protein autoubiquitination / Cul4-RING E3 ubiquitin ligase complex / UV-damage excision repair / protein neddylation / regulation of JNK cascade / metal-dependent deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases) / NEDD8 ligase activity / Cul5-RING ubiquitin ligase complex / biological process involved in interaction with symbiont / negative regulation of response to oxidative stress / RHOBTB1 GTPase cycle / regulation of mitotic cell cycle phase transition / ubiquitin-ubiquitin ligase activity / Cul4A-RING E3 ubiquitin ligase complex / SCF ubiquitin ligase complex / inner cell mass cell proliferation / Cul2-RING ubiquitin ligase complex / WD40-repeat domain binding / ubiquitin ligase complex scaffold activity / Cul4B-RING E3 ubiquitin ligase complex / negative regulation of type I interferon production / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / Cul3-RING ubiquitin ligase complex / positive regulation of G1/S transition of mitotic cell cycle / negative regulation of reproductive process / negative regulation of developmental process / skeletal muscle cell differentiation / protein monoubiquitination / TGF-beta receptor signaling activates SMADs / cullin family protein binding / somatic stem cell population maintenance / hemopoiesis / viral release from host cell / response to light stimulus / anatomical structure morphogenesis / ectopic germ cell programmed cell death / proteasomal protein catabolic process / protein K48-linked ubiquitination / positive regulation of viral genome replication / post-translational protein modification / ubiquitin ligase complex / JNK cascade / positive regulation of gluconeogenesis / positive regulation of TORC1 signaling / T cell activation / translation initiation factor activity / intrinsic apoptotic signaling pathway / cellular response to amino acid stimulus Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.8 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_3315.map.gz | 36 MB | EMDB map data format | |
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Header (meta data) | emd-3315-v30.xml emd-3315.xml | 19.5 KB 19.5 KB | Display Display | EMDB header |
Images | emd_3315.png | 97.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3315 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3315 | HTTPS FTP |
-Validation report
Summary document | emd_3315_validation.pdf.gz | 246.5 KB | Display | EMDB validaton report |
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Full document | emd_3315_full_validation.pdf.gz | 245.6 KB | Display | |
Data in XML | emd_3315_validation.xml.gz | 6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3315 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3315 | 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_3315.map.gz / Format: CCP4 / Size: 39.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM structure of CSN-N8-CRL4A at 8.8 A resolution | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.32 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-CRL4A complex
+Supramolecule #1000: Recombinant human CSN-N8-CRL4A 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: CUL4A
+Macromolecule #10: DNA DAMAGE-BINDING PROTEIN 1
+Macromolecule #11: E3 UBIQUITIN-PROTEIN LIGASE RBX1
+Macromolecule #12: NEDD8
-Experimental details
-Structure determination
Method | cryo EM |
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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 |
Grid | Details: Quantifoil holey carbon grids (R1.2/1.3, Cu 400 mesh) and Lacey carbons films |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 93 K / Instrument: LEICA EM GP / Method: Blot for 2 seconds before plunging |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: Gatan Image Filter Quantum LS / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV |
Date | Jun 1, 2015 |
Image recording | Category: CCD / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number real images: 2626 Details: Every image is the average of 38 frames recorded by the direct electron detector |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.5 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Details | To obtain this homogeneous set of particles we used 3D focus classification on CSN with signal subtraction of CUL4A-DDB1. |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 8.8 Å / Resolution method: OTHER / Software - Name: EMAN2, RELION / Number images used: 19041 |
-Atomic model buiding 1
Initial model | PDB ID: |
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Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
-Atomic model buiding 2
Initial model | PDB ID: |
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Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
-Atomic model buiding 3
Initial model | PDB ID: |
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Refinement | Space: REAL / Protocol: FLEXIBLE FIT |