+Open data
-Basic information
Entry | Database: PDB / ID: 7un6 | ||||||||||||||||||
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Title | Complex of UBE2O with NAP1L1 | ||||||||||||||||||
Components |
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Keywords | CYTOSOLIC PROTEIN / Ubiquitylation | ||||||||||||||||||
Function / homology | Function and homology information histone chaperone activity / (E3-independent) E2 ubiquitin-conjugating enzyme / positive regulation of BMP signaling pathway / positive regulation of neural precursor cell proliferation / retrograde transport, endosome to Golgi / positive regulation of neurogenesis / protein monoubiquitination / ubiquitin conjugating enzyme activity / protein K63-linked ubiquitination / ubiquitin-protein transferase activity ...histone chaperone activity / (E3-independent) E2 ubiquitin-conjugating enzyme / positive regulation of BMP signaling pathway / positive regulation of neural precursor cell proliferation / retrograde transport, endosome to Golgi / positive regulation of neurogenesis / protein monoubiquitination / ubiquitin conjugating enzyme activity / protein K63-linked ubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / nucleosome assembly / melanosome / Antigen processing: Ubiquitination & Proteasome degradation / nervous system development / histone binding / DNA replication / nuclear body / chromatin binding / positive regulation of cell population proliferation / chromatin / RNA binding / nucleoplasm / ATP binding / membrane / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | ||||||||||||||||||
Authors | Yip, M.C.J. / Sedor, S.F. / Shao, S. | ||||||||||||||||||
Funding support | United States, 5items
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Citation | Journal: Nat Struct Mol Biol / Year: 2022 Title: Mechanism of client selection by the protein quality-control factor UBE2O. Authors: Matthew C J Yip / Samantha F Sedor / Sichen Shao / Abstract: The E2/E3 enzyme UBE2O ubiquitylates diverse clients to mediate important processes, including targeting unassembled 'orphan' proteins for quality control and clearing ribosomes during erythropoiesis. ...The E2/E3 enzyme UBE2O ubiquitylates diverse clients to mediate important processes, including targeting unassembled 'orphan' proteins for quality control and clearing ribosomes during erythropoiesis. How quality-control factors, such as UBE2O, select clients on the basis of heterogeneous features is largely unknown. Here, we show that UBE2O client selection is regulated by ubiquitin binding and a cofactor, NAP1L1. Attaching a single ubiquitin onto a client enhances UBE2O binding and multi-mono-ubiquitylation. UBE2O also repurposes the histone chaperone NAP1L1 as an adapter to recruit a subset of clients. Cryo-EM structures of human UBE2O in complex with NAP1L1 reveal a malleable client recruitment interface that is autoinhibited by the intrinsically reactive UBC domain. Adding a ubiquitylated client identifies a distinct ubiquitin-binding SH3-like domain required for client selection. Our findings reveal how multivalency and a feed-forward mechanism drive the selection of protein quality-control clients. | ||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7un6.cif.gz | 230.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7un6.ent.gz | 169.6 KB | Display | PDB format |
PDBx/mmJSON format | 7un6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7un6_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7un6_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7un6_validation.xml.gz | 49 KB | Display | |
Data in CIF | 7un6_validation.cif.gz | 72.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/un/7un6 ftp://data.pdbj.org/pub/pdb/validation_reports/un/7un6 | HTTPS FTP |
-Related structure data
Related structure data | 26614MC 7un3C C: citing same article (ref.) M: map data used to model this data |
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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: 147187.188 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2O, KIAA1734 / Production host: Homo sapiens (human) References: UniProt: Q9C0C9, (E3-independent) E2 ubiquitin-conjugating enzyme |
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#2: Protein | Mass: 48363.898 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NAP1L1, NRP / Production host: Homo sapiens (human) / References: UniProt: P55209 |
-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: Complex of UBE2O with NAP1L1 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1400 nm |
Image recording | Electron dose: 57.4 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 447881 / Symmetry type: POINT |