Cryo-EM structure of the Ams1 and Nbr1 complex

Experimental Data Snapshot

  • Resolution: 2.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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Molecular and structural mechanisms of ZZ domain-mediated cargo selection by Nbr1.

Wang, Y.Y.Zhang, J.Liu, X.M.Li, Y.Sui, J.Dong, M.Q.Ye, K.Du, L.L.

(2021) EMBO J 40: e107497-e107497

  • DOI: https://doi.org/10.15252/embj.2020107497
  • Primary Citation of Related Structures:  
    7DD9, 7DDE

  • PubMed Abstract: 

    In selective autophagy, cargo selectivity is determined by autophagy receptors. However, it remains scarcely understood how autophagy receptors recognize specific protein cargos. In the fission yeast Schizosaccharomyces pombe, a selective autophagy pathway termed Nbr1-mediated vacuolar targeting (NVT) employs Nbr1, an autophagy receptor conserved across eukaryotes including humans, to target cytosolic hydrolases into the vacuole. Here, we identify two new NVT cargos, the mannosidase Ams1 and the aminopeptidase Ape4, that bind competitively to the first ZZ domain of Nbr1 (Nbr1-ZZ1). High-resolution cryo-EM analyses reveal how a single ZZ domain recognizes two distinct protein cargos. Nbr1-ZZ1 not only recognizes the N-termini of cargos via a conserved acidic pocket, similar to other characterized ZZ domains, but also engages additional parts of cargos in a cargo-specific manner. Our findings unveil a single-domain bispecific mechanism of autophagy cargo recognition, elucidate its underlying structural basis, and expand the understanding of ZZ domain-mediated protein-protein interactions.

  • Organizational Affiliation

    College of Life Sciences, Beijing Normal University, Beijing, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Alpha-mannosidase,ZZ-type zinc finger-containing protein P35G2.11c,Maltose/maltodextrin-binding periplasmic proteinA,
B [auth C],
C [auth E],
D [auth G]
1,584Schizosaccharomyces pombe 972h-Escherichia coli K-12Mutation(s): 0 
Gene Names: ams1mns2SPAC513.05SPBP35G2.11cmalEb4034JW3994
Find proteins for Q9UT61 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore Q9UT61 
Go to UniProtKB:  Q9UT61
Find proteins for P0AEX9 (Escherichia coli (strain K12))
Explore P0AEX9 
Go to UniProtKB:  P0AEX9
Find proteins for Q9P792 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore Q9P792 
Go to UniProtKB:  Q9P792
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ9UT61P0AEX9Q9P792
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth C]
I [auth C]
E [auth A],
F [auth A],
G [auth A],
H [auth C],
I [auth C],
J [auth C],
K [auth E],
L [auth E],
M [auth E],
N [auth G],
O [auth G],
P [auth G]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32071199, 91940302
Chinese Academy of SciencesChinaXDB37010201
National Basic Research Program of China (973 Program)China2017YFA0504600

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-14
    Type: Initial release
  • Version 1.1: 2021-08-11
    Changes: Database references