8GH6 | pdb_00008gh6

Bombyx mori R2 retrotransposon initiating target-primed reverse transcription


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.08 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history

Literature

Structure of the R2 non-LTR retrotransposon initiating target-primed reverse transcription.

Wilkinson, M.E.Frangieh, C.J.Macrae, R.K.Zhang, F.

(2023) Science 380: 301-308

  • DOI: https://doi.org/10.1126/science.adg7883
  • Primary Citation Related Structures: 
    8GH6

  • PubMed Abstract: 

    Non-long terminal repeat (non-LTR) retrotransposons, or long interspersed nuclear elements (LINEs), are an abundant class of eukaryotic transposons that insert into genomes by target-primed reverse transcription (TPRT). During TPRT, a target DNA sequence is nicked and primes reverse transcription of the retrotransposon RNA. Here, we report the cryo-electron microscopy structure of the Bombyx mori R2 non-LTR retrotransposon initiating TPRT at its ribosomal DNA target. The target DNA sequence is unwound at the insertion site and recognized by an upstream motif. An extension of the reverse transcriptase (RT) domain recognizes the retrotransposon RNA and guides the 3' end into the RT active site to template reverse transcription. We used Cas9 to retarget R2 in vitro to non-native sequences, suggesting future use as a reprogrammable RNA-based gene-insertion tool.


  • Organizational Affiliation
    • Howard Hughes Medical Institute, Cambridge, MA 02139, USA.

Macromolecule Content 

  • Total Structure Weight: 255.81 kDa 
  • Atom Count: 10,785 
  • Modeled Residue Count: 1,075 
  • Deposited Residue Count: 1,531 
  • Unique protein chains: 1
  • Unique nucleic acid chains: 4

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Reverse transcriptase-like protein1,114Bombyx moriMutation(s): 0 
UniProt
Find proteins for V9H052 (Bombyx mori)
Explore V9H052 
Go to UniProtKB:  V9H052
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupV9H052
Sequence Annotations
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Reference Sequence
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Entity ID: 2
MoleculeChains LengthOrganismImage
28S DNA bottom strand, 3' side70Bombyx mori
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Reference Sequence
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Entity ID: 3
MoleculeChains LengthOrganismImage
28S DNA bottom strand, 5' side (priming strand)C [auth P]24Bombyx mori
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Reference Sequence
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Entity ID: 4
MoleculeChains LengthOrganismImage
R2Bm 3'UTR RNAD [auth R]253Bombyx mori
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Reference Sequence
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Entity ID: 5
MoleculeChains LengthOrganismImage
28S DNA top strandE [auth T]70Bombyx mori
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.08 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION4.0
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesR01HG009761

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-05
    Type: Initial release
  • Version 1.1: 2023-04-12
    Changes: Database references
  • Version 1.2: 2023-04-19
    Changes: Database references
  • Version 1.3: 2023-05-03
    Changes: Database references
  • Version 1.4: 2023-08-16
    Changes: Data collection, Other