7MEX

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.35 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: https://doi.org/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. 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

    Tsinghua-Peking Center for Life Sciences, Department of Chemistry, Tsinghua University, Beijing, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
UbiquitinA [auth C]76Homo sapiensMutation(s): 1 
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG48 (Homo sapiens)
Explore P0CG48 
Go to UniProtKB:  P0CG48
GTEx:  ENSG00000150991 
Entity Groups  
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UniProt GroupP0CG48
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-conjugating enzyme E2 2150Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RAD6UBC2YGL058W
EC: 2.3.2.23
UniProt
Find proteins for P06104 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P06104 
Go to UniProtKB:  P06104
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UniProt GroupP06104
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
N-degronC [auth D]43Saccharomyces cerevisiae S288CMutation(s): 0 
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase UBR1D [auth A]1,950Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UBR1PTR1YGR184CG7168
EC: 2.3.2.27
UniProt
Find proteins for P19812 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P19812 
Go to UniProtKB:  P19812
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UniProt GroupP19812
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.35 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1
MODEL REFINEMENTPHENIX

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