7NKU | pdb_00007nku

diazaborine bound Drg1(AFG2)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 7NKU

This is version 1.2 of the entry. See complete history

Literature

Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine.

Prattes, M.Grishkovskaya, I.Hodirnau, V.V.Rossler, I.Klein, I.Hetzmannseder, C.Zisser, G.Gruber, C.C.Gruber, K.Haselbach, D.Bergler, H.

(2021) Nat Commun 12: 3483-3483

  • DOI: https://doi.org/10.1038/s41467-021-23854-x
  • Primary Citation Related Structures: 
    7NKU

  • PubMed Abstract: 

    The hexameric AAA-ATPase Drg1 is a key factor in eukaryotic ribosome biogenesis and initiates cytoplasmic maturation of the large ribosomal subunit by releasing the shuttling maturation factor Rlp24. Drg1 monomers contain two AAA-domains (D1 and D2) that act in a concerted manner. Rlp24 release is inhibited by the drug diazaborine which blocks ATP hydrolysis in D2. The mode of inhibition was unknown. Here we show the first cryo-EM structure of Drg1 revealing the inhibitory mechanism. Diazaborine forms a covalent bond to the 2'-OH of the nucleotide in D2, explaining its specificity for this site. As a consequence, the D2 domain is locked in a rigid, inactive state, stalling the whole Drg1 hexamer. Resistance mechanisms identified include abolished drug binding and altered positioning of the nucleotide. Our results suggest nucleotide-modifying compounds as potential novel inhibitors for AAA-ATPases.


  • Organizational Affiliation
    • Institute of Molecular Biosciences, University of Graz, Graz, Austria.

Macromolecule Content 

  • Total Structure Weight: 517.02 kDa 
  • Atom Count: 25,332 
  • Modeled Residue Count: 3,252 
  • Deposited Residue Count: 4,680 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ATPase family gene 2 protein
A, B, C, D, E
A, B, C, D, E, F
780Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: AFG2DRG1YLR397CL8084.16
EC: 3.6.4.10
UniProt
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
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AGS

Query on AGS



Download:Ideal Coordinates CCD File
G [auth A]
H [auth A]
K [auth B]
L [auth B]
N [auth C]
G [auth A],
H [auth A],
K [auth B],
L [auth B],
N [auth C],
O [auth C],
Q [auth D],
R [auth D],
T [auth E],
U [auth E],
W [auth F],
X [auth F]
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
C10 H16 N5 O12 P3 S
NLTUCYMLOPLUHL-KQYNXXCUSA-N
TDB
(Subject of Investigation/LOI)

Query on TDB



Download:Ideal Coordinates CCD File
I [auth A]
J [auth A]
M [auth C]
P [auth D]
S [auth D]
I [auth A],
J [auth A],
M [auth C],
P [auth D],
S [auth D],
V [auth F]
6-METHYL-2(PROPANE-1-SULFONYL)-2H-THIENO[3,2-D][1,2,3]DIAZABORININ-1-OL
C9 H13 B N2 O3 S2
TVXLILKNSPCVRB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC
MODEL REFINEMENTRosetta
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-23
    Type: Initial release
  • Version 1.1: 2025-04-09
    Changes: Data collection, Database references, Structure summary
  • Version 1.2: 2025-10-01
    Changes: Advisory, Data collection, Derived calculations