9D4S | pdb_00009d4s

Structure of G2L4 RT in complex with 15 nucleotide snapback substrate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.77 Å
  • R-Value Free: 
    0.277 (Depositor), 0.275 (DCC) 
  • R-Value Work: 
    0.235 (Depositor), 0.236 (DCC) 
  • R-Value Observed: 
    0.238 (Depositor) 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

Structural basis for the evolution of a domesticated group II intron-like reverse transcriptase to function in host cell DNA repair.

Park, S.K.Guo, M.Stamos, J.L.Kim, W.Lee, S.Zhang, Y.J.Lambowitz, A.M.

(2025) Proc Natl Acad Sci U S A 122: e2504208122-e2504208122

  • DOI: https://doi.org/10.1073/pnas.2504208122
  • Primary Citation of Related Structures:  
    9D4S, 9D5X

  • PubMed Abstract: 

    A previous study found that a bacterial group II intron-like reverse transcriptase (G2L4 RT) evolved to function in double-strand break repair (DSBR) via microhomology-mediated end-joining (MMEJ) and that a mobile group II intron-encoded RT has a basal DSBR activity that uses conserved structural features of non-long terminal repeat (non-LTR)-retroelement RTs. Here, we determined G2L4 RT apoenzyme and snap-back DNA synthesis structures revealing unique structural adaptations that optimized its cellular function in DSBR. These included an RT3a structure that stabilizes the apoenzyme in an inactive conformation until encountering a DNA substrate; a longer N-terminal extension/RT0-loop with conserved residues that together with a modified active site favors strand annealing; and a conserved dimer interface that localizes G2L4 RT homodimers to DSBR sites with both monomers positioned for MMEJ. Our findings reveal how an RT can function in DNA repair and suggest ways of optimizing related RTs for genome engineering applications.


  • Organizational Affiliation
    • Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712.

Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Group II intron-like 4 reverse transcriptaseA,
C [auth B]
408GammaproteobacteriaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNAB [auth C],
D [auth P]
18synthetic construct
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.77 Å
  • R-Value Free:  0.277 (Depositor), 0.275 (DCC) 
  • R-Value Work:  0.235 (Depositor), 0.236 (DCC) 
  • R-Value Observed: 0.238 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.398α = 90
b = 99.19β = 90
c = 157.276γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35148356

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-30
    Type: Initial release
  • Version 1.1: 2025-08-13
    Changes: Database references