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- PDB-7un6: Complex of UBE2O with NAP1L1 -

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Basic information

Entry
Database: PDB / ID: 7un6
TitleComplex of UBE2O with NAP1L1
Components
  • (E3-independent) E2 ubiquitin-conjugating enzyme
  • Nucleosome assembly protein 1-like 1
KeywordsCYTOSOLIC 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 / ubiquitin conjugating enzyme activity / protein K63-linked ubiquitination / protein monoubiquitination / 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 / ubiquitin conjugating enzyme activity / protein K63-linked ubiquitination / protein monoubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / melanosome / Antigen processing: Ubiquitination & Proteasome degradation / nervous system development / nucleosome assembly / histone binding / DNA replication / nuclear body / positive regulation of cell population proliferation / chromatin binding / chromatin / RNA binding / nucleoplasm / ATP binding / nucleus / membrane / cytoplasm / cytosol
Similarity search - Function
UBE2O, ubiquitin binding SH3-C domain / UBE2O, tandem tSH3-B domain / UBE2O, N-terminal SH3-A domain / UBE2O, SH3-B domain / Nucleosome assembly protein (NAP) / NAP-like superfamily / Nucleosome assembly protein (NAP) / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. ...UBE2O, ubiquitin binding SH3-C domain / UBE2O, tandem tSH3-B domain / UBE2O, N-terminal SH3-A domain / UBE2O, SH3-B domain / Nucleosome assembly protein (NAP) / NAP-like superfamily / Nucleosome assembly protein (NAP) / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like
Similarity search - Domain/homology
Nucleosome assembly protein 1-like 1 / (E3-independent) E2 ubiquitin-conjugating enzyme
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsYip, M.C.J. / Sedor, S.F. / Shao, S.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)DP2GM137415 United States
David and Lucile Packard Foundation2019-69660 United States
Other privateVallee Foundation
American Heart Association287375208 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)F31HL157976 United States
CitationJournal: 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
DepositionApr 9, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Aug 17, 2022Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Aug 24, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: (E3-independent) E2 ubiquitin-conjugating enzyme
B: Nucleosome assembly protein 1-like 1
C: Nucleosome assembly protein 1-like 1


Theoretical massNumber of molelcules
Total (without water)243,9153
Polymers243,9153
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: immunoprecipitation
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein (E3-independent) E2 ubiquitin-conjugating enzyme / E2/E3 hybrid ubiquitin-protein ligase UBE2O / Ubiquitin carrier protein O / Ubiquitin-conjugating ...E2/E3 hybrid ubiquitin-protein ligase UBE2O / Ubiquitin carrier protein O / Ubiquitin-conjugating enzyme E2 O / Ubiquitin-conjugating enzyme E2 of 230 kDa / Ubiquitin-conjugating enzyme E2-230K / Ubiquitin-protein ligase O


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
#2: Protein Nucleosome assembly protein 1-like 1 / NAP-1-related protein / hNRP


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

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Complex of UBE2O with NAP1L1 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1400 nm
Image recordingElectron dose: 57.4 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 447881 / Symmetry type: POINT

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