6PQU

Cryo-EM structure of HzTransib/nicked TIR substrate DNA pre-reaction complex (PRC)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structures of a RAG-like transposase during cut-and-paste transposition.

Liu, C.Yang, Y.Schatz, D.G.

(2019) Nature 575: 540-544

  • DOI: https://doi.org/10.1038/s41586-019-1753-7
  • Primary Citation of Related Structures:  
    6PQN, 6PQR, 6PQU, 6PQX, 6PQY, 6PR5

  • PubMed Abstract: 

    Transposons have had a pivotal role in genome evolution 1 and are believed to be the evolutionary progenitors of the RAG1-RAG2 recombinase 2 , an essential component of the adaptive immune system in jawed vertebrates 3 . Here we report one crystal structure and five cryo-electron microscopy structures of Transib 4,5 , a RAG1-like transposase from Helicoverpa zea, that capture the entire transposition process from the apo enzyme to the terminal strand transfer complex with transposon ends covalently joined to target DNA, at resolutions of 3.0-4.6 Å. These structures reveal a butterfly-shaped complex that undergoes two cycles of marked conformational changes in which the 'wings' of the transposase unfurl to bind substrate DNA, close to execute cleavage, open to release the flanking DNA and close again to capture and attack target DNA. Transib possesses unique structural elements that compensate for the absence of a RAG2 partner, including a loop that interacts with the transposition target site and an accordion-like C-terminal tail that elongates and contracts to help to control the opening and closing of the enzyme and assembly of the active site. Our findings reveal the detailed reaction pathway of a eukaryotic cut-and-paste transposase and illuminate some of the earliest steps in the evolution of the RAG recombinase.


  • Organizational Affiliation

    Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-mediated transposase
A, E
497Helicoverpa zeaMutation(s): 0 
UniProt
Find proteins for B0F0C5 (Helicoverpa zea)
Explore B0F0C5 
Go to UniProtKB:  B0F0C5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB0F0C5
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(P*AP*TP*CP*TP*GP*GP*CP*CP*TP*AP*GP*AP*TP*CP*T)-3')
B, F
16Helicoverpa zea
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(P*CP*AP*CP*GP*GP*TP*GP*GP*AP*TP*CP*GP*AP*AP*AP*A)-3')
C, G
16Helicoverpa zea
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains LengthOrganismImage
TIR substrate DNA transferred strand
D, H
32Helicoverpa zea
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.15
RECONSTRUCTIONRELION3.0

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States1R01AI137079

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-09
    Type: Initial release
  • Version 1.1: 2019-11-27
    Changes: Database references
  • Version 1.2: 2019-12-04
    Changes: Database references
  • Version 1.3: 2019-12-18
    Changes: Author supporting evidence
  • Version 1.4: 2024-03-20
    Changes: Data collection, Database references, Refinement description