+Open data
-Basic information
Entry | Database: PDB / ID: 8bja | ||||||
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Title | Structure of the human UBR5 Dimer. | ||||||
Components | E3 ubiquitin-protein ligase UBR5 | ||||||
Keywords | LIGASE / UBR5 / E3 Ligase / nuclear / Degradation / Ubiquitin | ||||||
Function / homology | Function and homology information heterochromatin boundary formation / HECT-type E3 ubiquitin transferase / DNA repair-dependent chromatin remodeling / ubiquitin-ubiquitin ligase activity / progesterone receptor signaling pathway / protein K48-linked ubiquitination / ubiquitin binding / positive regulation of protein import into nucleus / protein polyubiquitination / ubiquitin protein ligase activity ...heterochromatin boundary formation / HECT-type E3 ubiquitin transferase / DNA repair-dependent chromatin remodeling / ubiquitin-ubiquitin ligase activity / progesterone receptor signaling pathway / protein K48-linked ubiquitination / ubiquitin binding / positive regulation of protein import into nucleus / protein polyubiquitination / ubiquitin protein ligase activity / positive regulation of canonical Wnt signaling pathway / DNA repair / DNA damage response / positive regulation of gene expression / perinuclear region of cytoplasm / protein-containing complex / RNA binding / zinc ion binding / nucleoplasm / membrane / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å | ||||||
Authors | Hodakova, Z. / Grishkovskaya, I. / Haselbach, D. | ||||||
Funding support | European Union, 1items
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Citation | Journal: EMBO J / Year: 2023 Title: Cryo-EM structure of the chain-elongating E3 ubiquitin ligase UBR5. Authors: Zuzana Hodáková / Irina Grishkovskaya / Hanna L Brunner / Derek L Bolhuis / Katarina Belačić / Alexander Schleiffer / Harald Kotisch / Nicholas G Brown / David Haselbach / Abstract: UBR5 is a nuclear E3 ligase that ubiquitinates a vast range of substrates for proteasomal degradation. This HECT domain-containing ubiquitin ligase has recently been identified as an important ...UBR5 is a nuclear E3 ligase that ubiquitinates a vast range of substrates for proteasomal degradation. This HECT domain-containing ubiquitin ligase has recently been identified as an important regulator of oncogenes, e.g., MYC, but little is known about its structure or mechanisms of substrate engagement and ubiquitination. Here, we present the cryo-EM structure of human UBR5, revealing an α-solenoid scaffold with numerous protein-protein interacting motifs, assembled into an antiparallel dimer that adopts further oligomeric states. Using cryo-EM processing tools, we observe the dynamic nature of the UBR5 catalytic domain, which we postulate is important for its enzymatic activity. We characterise the proteasomal nuclear import factor AKIRIN2 as an interacting protein and propose UBR5 as an efficient ubiquitin chain elongator. This preference for ubiquitinated substrates and several distinct domains for protein-protein interactions may explain how UBR5 is linked to several different signalling pathways and cancers. Together, our data expand on the limited knowledge of the structure and function of HECT E3 ligases. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8bja.cif.gz | 664 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8bja.ent.gz | 515.6 KB | Display | PDB format |
PDBx/mmJSON format | 8bja.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8bja_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 8bja_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 8bja_validation.xml.gz | 90.1 KB | Display | |
Data in CIF | 8bja_validation.cif.gz | 136.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bj/8bja ftp://data.pdbj.org/pub/pdb/validation_reports/bj/8bja | HTTPS FTP |
-Related structure data
Related structure data | 16087MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 312810.906 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UBR5, EDD, EDD1, HYD, KIAA0896 / Cell (production host): HEK 293T / Cell line (production host): HEK293 / Production host: Homo sapiens (human) References: UniProt: O95071, HECT-type E3 ubiquitin transferase #2: Chemical | ChemComp-ZN / Has ligand of interest | Y | |
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-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: UBR5 / Type: ORGANELLE OR CELLULAR COMPONENT / Details: Homodimer / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Value: 310 kDa/nm / Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Homo sapiens (human) / Cell: HEK 293T |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: YES / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil |
EM embedding | Details: Sample vitrified using a final concentration of 4mM CHAPSO or 0.005% fluorinated octyl beta-maltoside Material: CHAPSO, fOG |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) |
-Processing
CTF correction | Type: NONE | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 3 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 288287 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | B value: 104 / Space: REAL | ||||||||||||||||||||||||
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