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- PDB-6r7f: Structural basis of Cullin-2 RING E3 ligase regulation by the COP... -
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Basic information
Entry | Database: PDB / ID: 6r7f | ||||||
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Title | Structural basis of Cullin-2 RING E3 ligase regulation by the COP9 signalosome | ||||||
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![]() | LIGASE / Cullin-Ring E3 Ligase COP9 signalosome neddylation | ||||||
Function / homology | ![]() COP9 signalosome assembly / trophectodermal cell proliferation / macrophage migration inhibitory factor binding / regulation of IRE1-mediated unfolded protein response / exosomal secretion / GTPase inhibitor activity / deNEDDylase activity / protein deneddylation / regulation of protein neddylation / eukaryotic translation initiation factor 3 complex ...COP9 signalosome assembly / trophectodermal cell proliferation / macrophage migration inhibitory factor binding / regulation of IRE1-mediated unfolded protein response / exosomal secretion / GTPase inhibitor activity / deNEDDylase activity / protein deneddylation / regulation of protein neddylation / eukaryotic translation initiation factor 3 complex / activation of NF-kappaB-inducing kinase activity / regulation of cellular response to hypoxia / cullin-RING-type E3 NEDD8 transferase / NEDD8 transferase activity / RHOBTB3 ATPase cycle / COP9 signalosome / negative regulation of receptor signaling pathway via JAK-STAT / cullin-RING ubiquitin ligase complex / cellular response to chemical stress / Cul7-RING ubiquitin ligase complex / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / transcription elongation factor activity / target-directed miRNA degradation / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / VCB complex / elongin complex / positive regulation of protein autoubiquitination / protein neddylation / regulation of JNK cascade / Replication of the SARS-CoV-1 genome / Hydrolases; Acting on peptide bonds (peptidases) / metal-dependent deubiquitinase activity / NEDD8 ligase activity / RHOBTB1 GTPase cycle / negative regulation of response to oxidative stress / Cul5-RING ubiquitin ligase complex / regulation of DNA damage response, signal transduction by p53 class mediator / SCF ubiquitin ligase complex / inner cell mass cell proliferation / Cul2-RING ubiquitin ligase complex / intracellular membraneless organelle / ubiquitin-ubiquitin ligase activity / Cul4A-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 / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / SUMOylation of ubiquitinylation proteins / negative regulation of mitophagy / Prolactin receptor signaling / TGF-beta receptor signaling activates SMADs / cullin family protein binding / response to light stimulus / skeletal muscle cell differentiation / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / negative regulation of transcription elongation by RNA polymerase II / regulation of proteolysis / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / regulation of postsynapse assembly / anatomical structure morphogenesis / protein monoubiquitination / Tat-mediated elongation of the HIV-1 transcript / ubiquitin-like ligase-substrate adaptor activity / negative regulation of signal transduction / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / protein K48-linked ubiquitination / RNA Polymerase II Transcription Elongation / Nuclear events stimulated by ALK signaling in cancer / Formation of RNA Pol II elongation complex / positive regulation of DNA-binding transcription factor activity / JNK cascade / negative regulation of TORC1 signaling / RNA Polymerase II Pre-transcription Events / regulation of cellular response to insulin stimulus / translation initiation factor activity / positive regulation of TORC1 signaling / post-translational protein modification / negative regulation of autophagy / intrinsic apoptotic signaling pathway / negative regulation of insulin receptor signaling pathway / protein serine/threonine kinase binding / T cell activation / Regulation of BACH1 activity / transcription corepressor binding / positive regulation of cell differentiation / cellular response to amino acid stimulus / transcription initiation at RNA polymerase II promoter / TP53 Regulates Transcription of DNA Repair Genes / Degradation of DVL / transcription elongation by RNA polymerase II / Degradation of GLI1 by the proteasome / negative regulation of canonical Wnt signaling pathway / Recognition of DNA damage by PCNA-containing replication complex / Iron uptake and transport / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Negative regulation of NOTCH4 signaling Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8.2 Å | ||||||
![]() | Faull, S.V. / Lau, A.M.C. / Martens, C. / Ahdash, Z. / Yebenes, H. / Schmidt, C. / Beuron, F. / Cronin, N.B. / Morris, E.P. / Politis, A. | ||||||
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![]() | ![]() Title: Structural basis of Cullin 2 RING E3 ligase regulation by the COP9 signalosome. Authors: Sarah V Faull / Andy M C Lau / Chloe Martens / Zainab Ahdash / Kjetil Hansen / Hugo Yebenes / Carla Schmidt / Fabienne Beuron / Nora B Cronin / Edward P Morris / Argyris Politis / ![]() ![]() ![]() Abstract: Cullin-Ring E3 Ligases (CRLs) regulate a multitude of cellular pathways through specific substrate receptors. The COP9 signalosome (CSN) deactivates CRLs by removing NEDD8 from activated Cullins. ...Cullin-Ring E3 Ligases (CRLs) regulate a multitude of cellular pathways through specific substrate receptors. The COP9 signalosome (CSN) deactivates CRLs by removing NEDD8 from activated Cullins. Here we present structures of the neddylated and deneddylated CSN-CRL2 complexes by combining single-particle cryo-electron microscopy (cryo-EM) with chemical cross-linking mass spectrometry (XL-MS). These structures suggest a conserved mechanism of CSN activation, consisting of conformational clamping of the CRL2 substrate by CSN2/CSN4, release of the catalytic CSN5/CSN6 heterodimer and finally activation of the CSN5 deneddylation machinery. Using hydrogen-deuterium exchange (HDX)-MS we show that CRL2 activates CSN5/CSN6 in a neddylation-independent manner. The presence of NEDD8 is required to activate the CSN5 active site. Overall, by synergising cryo-EM with MS, we identify sensory regions of the CSN that mediate its stepwise activation and provide a framework for understanding the regulatory mechanism of other Cullin family members. | ||||||
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 720.3 KB | Display | ![]() |
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PDB format | ![]() | 558.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 878.5 KB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 105.1 KB | Display | |
Data in CIF | ![]() | 167.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4739MC ![]() 4736C ![]() 4741C ![]() 4742C ![]() 4744C ![]() 6r6hC ![]() 6r7hC ![]() 6r7iC ![]() 6r7nC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
-COP9 signalosome complex subunit ... , 8 types, 8 molecules ABCDEFHG
#1: Protein | Mass: 49253.535 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 51664.570 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Protein | Mass: 45808.816 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#4: Protein | Mass: 46322.688 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#5: Protein | Mass: 35184.059 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q92905, Hydrolases; Acting on peptide bonds (peptidases) |
#6: Protein | Mass: 32507.193 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#7: Protein | Mass: 23245.543 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#8: Protein | Mass: 23429.709 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Protein , 6 types, 6 molecules VPQORN
#9: Protein | Mass: 18558.162 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#10: Protein | Mass: 13147.781 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#11: Protein | Mass: 12485.135 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#12: Protein | Mass: 87098.930 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#13: Protein | Mass: 10655.229 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#14: Protein | Mass: 8573.978 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Ternary complex of COP9 signalosome (CSN) and neddylated Cullin-Ring E3 ligase CRL (cullin-2 with Rbx1, Elongin-B, Elongin-C and VHL) Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 7.5 Details: 15 mM HEPES pH 7.5 100 mM NaCL 0.5 mM DTT 1% Glycerol |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1800 nm / C2 aperture diameter: 100 µm |
Specimen holder | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 45 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
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Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 8.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 20055 / Symmetry type: POINT |