Cryo-EM structure of substrate engaged Drg1 hexamer

Experimental Data Snapshot

  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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Structural dynamics of AAA + ATPase Drg1 and mechanism of benzo-diazaborine inhibition.

Ma, C.Wu, D.Chen, Q.Gao, N.

(2022) Nat Commun 13: 6765-6765

  • DOI: https://doi.org/10.1038/s41467-022-34511-2
  • Primary Citation of Related Structures:  
    7WBB, 7WD3, 7YKK, 7YKL, 7YKT, 7YKZ

  • PubMed Abstract: 

    The type II AAA + ATPase Drg1 is a ribosome assembly factor, functioning to release Rlp24 from the pre-60S particle just exported from nucleus, and its activity in can be inhibited by a drug molecule diazaborine. However, molecular mechanisms of Drg1-mediated Rlp24 removal and diazaborine-mediated inhibition are not fully understood. Here, we report Drg1 structures in different nucleotide-binding and benzo-diazaborine treated states. Drg1 hexamers transits between two extreme conformations (planar or helical arrangement of protomers). By forming covalent adducts with ATP molecules in both ATPase domain, benzo-diazaborine locks Drg1 hexamers in a symmetric and non-productive conformation to inhibits both inter-protomer and inter-ring communication of Drg1 hexamers. We also obtained a substrate-engaged mutant Drg1 structure, in which conserved pore-loops form a spiral staircase to interact with the polypeptide through a sequence-independent manner. Structure-based mutagenesis data highlight the functional importance of the pore-loop, the D1-D2 linker and the inter-subunit signaling motif of Drg1, which share similar regulatory mechanisms with p97. Our results suggest that Drg1 may function as an unfoldase that threads a substrate protein within the pre-60S particle.

  • Organizational Affiliation

    State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Center for Life Sciences, School of Life Sciences, Peking University, 100871, Beijing, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
AFG2 isoform 1780Saccharomyces cerevisiaeMutation(s): 2 
Gene Names: AFG2
Find proteins for P32794 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32794 
Go to UniProtKB:  P32794
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32794
Sequence Annotations
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
substrateF [auth H]23Escherichia coliMutation(s): 0 
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP (Subject of Investigation/LOI)
Query on ATP

Download Ideal Coordinates CCD File 
H [auth A]
I [auth A]
J [auth B]
K [auth B]
L [auth D]
H [auth A],
I [auth A],
J [auth B],
K [auth B],
L [auth D],
M [auth D],
N [auth E],
O [auth E],
P [auth F],
Q [auth C],
R [auth C]
C10 H16 N5 O13 P3
Experimental Data & Validation

Experimental Data

  • Resolution: 3.60 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: 2022-12-28
    Type: Initial release