7MEY

Structure of yeast Ubr1 in complex with Ubc2 and monoubiquitinated N-degron


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.67 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural insights into Ubr1-mediated N-degron polyubiquitination.

Pan, M.Zheng, Q.Wang, T.Liang, L.Mao, J.Zuo, C.Ding, R.Ai, H.Xie, Y.Si, D.Yu, Y.Liu, L.Zhao, M.

(2021) Nature 600: 334-338

  • DOI: 10.1038/s41586-021-04097-8
  • Primary Citation of Related Structures:  
    7MEX, 7MEY

  • PubMed Abstract: 
  • The N-degron pathway targets proteins that bear a destabilizing residue at the N terminus for proteasome-dependent degradation 1 . In yeast, Ubr1-a single-subunit E3 ligase-is responsible for the Arg/N-degron pathway 2 . How Ubr1 mediates the initiation of ubiquitination and the elongation of the ubiquitin chain in a linkage-specific manner through a single E2 ubiquitin-conjugating enzyme (Ubc2) remains unknown ...

    The N-degron pathway targets proteins that bear a destabilizing residue at the N terminus for proteasome-dependent degradation 1 . In yeast, Ubr1-a single-subunit E3 ligase-is responsible for the Arg/N-degron pathway 2 . How Ubr1 mediates the initiation of ubiquitination and the elongation of the ubiquitin chain in a linkage-specific manner through a single E2 ubiquitin-conjugating enzyme (Ubc2) remains unknown. Here we developed chemical strategies to mimic the reaction intermediates of the first and second ubiquitin transfer steps, and determined the cryo-electron microscopy structures of Ubr1 in complex with Ubc2, ubiquitin and two N-degron peptides, representing the initiation and elongation steps of ubiquitination. Key structural elements, including a Ubc2-binding region and an acceptor ubiquitin-binding loop on Ubr1, were identified and characterized. These structures provide mechanistic insights into the initiation and elongation of ubiquitination catalysed by Ubr1.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA. mlzhao@uchicago.edu.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase UBR1A1,950Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UBR1PTR1YGR184CG7168
EC: 2.3.2.27
UniProt
Find proteins for P19812 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P19812
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UniProt GroupP19812
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
UbiquitinB [auth C]75Homo sapiensMutation(s): 1 
Gene Names: UBB
UniProt & NIH Common Fund Data Resources
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PHAROS:  P0CG47
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UniProt GroupP0CG47
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-conjugating enzyme E2 2C [auth B]172Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RAD6UBC2YGL058W
EC: 2.3.2.23
UniProt
Find proteins for P06104 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
UbiquitinD75Homo sapiensMutation(s): 0 
Gene Names: UBB
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG47 (Homo sapiens)
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PHAROS:  P0CG47
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UniProt GroupP0CG47
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Monoubiquitinated N-degronE [auth F]43Saccharomyces cerevisiae S288CMutation(s): 0 
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.67 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2021-11-24
    Type: Initial release
  • Version 1.1: 2021-12-01
    Changes: Database references
  • Version 1.2: 2021-12-22
    Changes: Database references