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Yorodumi- PDB-6v9i: cryo-EM structure of Cullin5 bound to RING-box protein 2 (Cul5-Rbx2) -
+Open data
-Basic information
Entry | Database: PDB / ID: 6v9i | ||||||
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Title | cryo-EM structure of Cullin5 bound to RING-box protein 2 (Cul5-Rbx2) | ||||||
Components |
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Keywords | LIGASE / E3 Ubiquitin Ligase / RING-box protein | ||||||
Function / homology | Function and homology information radial glia guided migration of Purkinje cell / cerebral cortex radially oriented cell migration / ERBB2 signaling pathway / Neddylation / cullin-RING ubiquitin ligase complex / Antigen processing: Ubiquitination & Proteasome degradation / protein neddylation / NEDD8 ligase activity / Cul5-RING ubiquitin ligase complex / IgG binding ...radial glia guided migration of Purkinje cell / cerebral cortex radially oriented cell migration / ERBB2 signaling pathway / Neddylation / cullin-RING ubiquitin ligase complex / Antigen processing: Ubiquitination & Proteasome degradation / protein neddylation / NEDD8 ligase activity / Cul5-RING ubiquitin ligase complex / IgG binding / SCF ubiquitin ligase complex / intrinsic apoptotic signaling pathway in response to oxidative stress / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / site of DNA damage / cullin family protein binding / apoptotic mitochondrial changes / intrinsic apoptotic signaling pathway / Vif-mediated degradation of APOBEC3G / calcium channel activity / Inactivation of CSF3 (G-CSF) signaling / Evasion by RSV of host interferon responses / Downregulation of ERBB2 signaling / G1/S transition of mitotic cell cycle / ubiquitin-protein transferase activity / activation of cysteine-type endopeptidase activity involved in apoptotic process / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / signaling receptor activity / Neddylation / protein-macromolecule adaptor activity / ubiquitin-dependent protein catabolic process / protein ubiquitination / ubiquitin protein ligase binding / negative regulation of apoptotic process / zinc ion binding / extracellular region / nucleoplasm / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Streptococcus sp. group G (bacteria) Homo sapiens (human) Mus musculus (house mouse) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.2 Å | ||||||
Authors | Komives, E.A. / Lumpkin, R.J. / Baker, R.W. / Leschziner, A.E. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Commun / Year: 2020 Title: Structure and dynamics of the ASB9 CUL-RING E3 Ligase. Authors: Ryan J Lumpkin / Richard W Baker / Andres E Leschziner / Elizabeth A Komives / Abstract: The Cullin 5 (CUL5) Ring E3 ligase uses adaptors Elongins B and C (ELOB/C) to bind different SOCS-box-containing substrate receptors, determining the substrate specificity of the ligase. The 18- ...The Cullin 5 (CUL5) Ring E3 ligase uses adaptors Elongins B and C (ELOB/C) to bind different SOCS-box-containing substrate receptors, determining the substrate specificity of the ligase. The 18-member ankyrin and SOCS box (ASB) family is the largest substrate receptor family. Here we report cryo-EM data for the substrate, creatine kinase (CKB) bound to ASB9-ELOB/C, and for full-length CUL5 bound to the RING protein, RBX2, which binds various E2s. To date, no full structures are available either for a substrate-bound ASB nor for CUL5. Hydrogen-deuterium exchange (HDX-MS) mapped onto a full structural model of the ligase revealed long-range allostery extending from the substrate through CUL5. We propose a revised allosteric mechanism for how CUL-E3 ligases function. ASB9 and CUL5 behave as rigid rods, connected through a hinge provided by ELOB/C transmitting long-range allosteric crosstalk from the substrate through CUL5 to the RBX2 flexible linker. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6v9i.cif.gz | 127.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6v9i.ent.gz | 81.9 KB | Display | PDB format |
PDBx/mmJSON format | 6v9i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v9/6v9i ftp://data.pdbj.org/pub/pdb/validation_reports/v9/6v9i | HTTPS FTP |
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-Related structure data
Related structure data | 21121MC 6v9hC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Antibody | Mass: 100456.500 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus sp. group G (bacteria), (gene. exp.) Homo sapiens (human) Gene: spg, CUL5, VACM1 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P06654, UniProt: Q93034 | ||
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#2: Protein | Mass: 12721.500 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rnf7, Rbx2, Sag / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WTZ1 | ||
#3: Chemical | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: cryo-EM structure of Cullin5 bound to RING-box protein 2 (Cul5-Rbx2) Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT |
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Molecular weight | Value: 0.1 MDa / Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Escherichia coli (E. coli) / Strain: BL21 |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: 4 second blot time, blot force 20 |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 36000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN |
Image recording | Average exposure time: 8 sec. / Electron dose: 59 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 5.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 46877 / Details: Non-uniform refinement in cryoSPARC v2 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||
Atomic model building |
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