7XYU

Crystal structure of ZER1 bound to TFLH degron

  • Classification: LIGASE
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2022-06-02 Released: 2022-12-21 
  • Deposition Author(s): Dong, C., Yan, X., Li, Y.
  • Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.304 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.251 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

CRL2 ZER1/ZYG11B recognizes small N-terminal residues for degradation.

Li, Y.Zhao, Y.Yan, X.Ye, C.Weirich, S.Zhang, B.Wang, X.Song, L.Jiang, C.Jeltsch, A.Dong, C.Mi, W.

(2022) Nat Commun 13: 7636-7636

  • DOI: https://doi.org/10.1038/s41467-022-35169-6
  • Primary Citation of Related Structures:  
    7XYS, 7XYT, 7XYU, 7XYV, 7XYW, 7XYX

  • PubMed Abstract: 

    N-degron pathway plays an important role in the protein quality control and maintenance of cellular protein homeostasis. ZER1 and ZYG11B, the substrate receptors of the Cullin 2-RING E3 ubiquitin ligase (CRL2), recognize N-terminal (Nt) glycine degrons and participate in the Nt-myristoylation quality control through the Gly/N-degron pathway. Here we show that ZER1 and ZYG11B can also recognize small Nt-residues other than glycine. Specifically, ZER1 binds better to Nt-Ser, -Ala, -Thr and -Cys than to -Gly, while ZYG11B prefers Nt-Gly but also has the capacity to recognize Nt-Ser, -Ala and -Cys in vitro. We found that Nt-Ser, -Ala and -Cys undergo Nt-acetylation catalyzed by Nt-acetyltransferase (NAT), thereby shielding them from recognition by ZER1/ZYG11B in cells. Instead, ZER1/ZYG11B readily targets a selection of small Nt-residues lacking Nt-acetylation for degradation in NAT-deficient cells, implicating its role in the Nt-acetylation quality control. Furthermore, we present the crystal structures of ZER1 and ZYG11B bound to various small Nt-residues and uncover the molecular mechanism of non-acetylated substrate recognition by ZER1 and ZYG11B.


  • Organizational Affiliation

    The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Medical University General Hospital, The Second Hospital of Tianjin Medical University, Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin, 300070, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein zer-1 homologA [auth B],
B [auth A],
C,
D
251Homo sapiensMutation(s): 0 
Gene Names: ZER1C9orf60ZYGZYG11BL
UniProt & NIH Common Fund Data Resources
Find proteins for Q7Z7L7 (Homo sapiens)
Explore Q7Z7L7 
Go to UniProtKB:  Q7Z7L7
PHAROS:  Q7Z7L7
GTEx:  ENSG00000160445 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7Z7L7
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.304 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.251 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.779α = 90
b = 67.779β = 90
c = 418.181γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31900865
National Natural Science Foundation of China (NSFC)China32071193
National Natural Science Foundation of China (NSFC)China81874039

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-21
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description