9HMM | pdb_00009hmm

Crystal structure of mouse ADAT2/ADAT3 tRNA deamination complex A180V mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 
    0.245 (Depositor), 0.241 (DCC) 
  • R-Value Work: 
    0.195 (Depositor), 0.198 (DCC) 
  • R-Value Observed: 
    0.198 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

ADAT3 variants disrupt the activity of the ADAT tRNA deaminase complex and impair neuronal migration.

Del-Pozo-Rodriguez, J.Tilly, P.Lecat, R.Vaca, H.R.Mosser, L.Brivio, E.Balla, T.Gomes, M.V.Ramos-Morales, E.Schwaller, N.Salinas-Giege, T.VanNoy, G.England, E.M.Kern Lovgren, A.O'Leary, M.Chopra, M.Meave Ojeda, N.Toosi, M.B.Eslahi, A.Alerasool, M.Mojarrad, M.Pais, L.S.Yeh, R.C.Gable, D.L.Hashem, M.O.Abdulwahab, F.Rakiz Alqurashi, M.Sbeih, L.Z.Adas Blanco, O.A.Khater, R.A.Oprea, G.Rad, A.Alzaidan, H.Aldhalaan, H.Tous, E.Alsagheir, A.Alowain, M.Tamim, A.Alfayez, K.Alhashem, A.Alnuzha, A.Kamel, M.Al-Awam, B.S.Elnaggar, W.Almenabawy, N.O'Donnell-Luria, A.Neil, J.E.Gleeson, J.G.Walsh, C.A.Alkuraya, F.S.AlAbdi, L.Elkhateeb, N.Selim, L.Srivastava, S.Nedialkova, D.D.Drouard, L.Romier, C.Bayam, E.Godin, J.D.

(2025) Brain 148: 3407-3421

  • DOI: https://doi.org/10.1093/brain/awaf109
  • Primary Citation of Related Structures:  
    9HMM

  • PubMed Abstract: 

    The ADAT2/ADAT3 (ADAT) complex catalyzes the adenosine to inosine modification at the wobble position of eukaryotic tRNAs. Mutations in ADAT3, the catalytically inactive subunit of the ADAT2/ADAT3 complex, have been identified in patients presenting with severe neurodevelopmental disorders. Yet, the physiological function of ADAT2/ADAT3 complex during brain development remains totally unknown. Here, we investigated the role of the ADAT2/ADAT3 complex in cortical development. First, we reported 21 neurodevelopmental disorders patients carrying biallelic variants in ADAT3. Second, we used structural, biochemical, and enzymatic assays to deeply characterize the impact of those variants on ADAT2/ADAT3 structure, biochemical properties, enzymatic activity and tRNAs editing and abundance. Finally, in vivo complementation assays were performed to correlate functional deficits with neuronal migration defects in the developing mouse cortex. Our results showed that maintaining a proper level of ADAT2/ADAT3 catalytic activity is essential for radial migration of projection neurons in the developing mouse cortex. We demonstrated that the identified ADAT3 variants significantly impaired the abundance and, for some, the activity of the complex, leading to a substantial decrease in I34 levels with direct consequence on their steady-state. We correlated the severity of the migration phenotype with the degree of the loss of function caused by the variants. Altogether, our results highlight the critical role of ADAT2/ADAT3 during cortical development and provide cellular and molecular insights into the pathogenic mechanisms underlying ADAT3-related neurodevelopmental disorders.


  • Organizational Affiliation
    • IGBMC, Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67400 Illkirch, France.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
tRNA-specific adenosine deaminase 2191Mus musculusMutation(s): 0 
Gene Names: Adat2Deadc1
EC: 3.5.4.33
UniProt & NIH Common Fund Data Resources
Find proteins for Q6P6J0 (Mus musculus)
Explore Q6P6J0 
Go to UniProtKB:  Q6P6J0
IMPC:  MGI:1914007
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6P6J0
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Probable inactive tRNA-specific adenosine deaminase-like protein 3320Mus musculusMutation(s): 1 
Gene Names: Adat3
UniProt
Find proteins for Q6PAT0 (Mus musculus)
Explore Q6PAT0 
Go to UniProtKB:  Q6PAT0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6PAT0
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free:  0.245 (Depositor), 0.241 (DCC) 
  • R-Value Work:  0.195 (Depositor), 0.198 (DCC) 
  • R-Value Observed: 0.198 (Depositor) 
Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.903α = 90
b = 106.398β = 90
c = 129.199γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Agence Nationale de la Recherche (ANR)FranceANR-21-CE12-0026

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-14
    Type: Initial release
  • Version 1.1: 2025-09-10
    Changes: Database references