6PR5

Cryo-EM structure of HzTransib strand transfer complex (STC)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.3 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.3 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: 10.1038/s41586-019-1753-7
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Transposons have had a pivotal role in genome evolution <sup>1 </sup> and are believed to be the evolutionary progenitors of the RAG1-RAG2 recombinase <sup>2 </sup>, an essential component of the adaptive immune system in jawed vertebrates <sup>3 </s ...

    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 Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA.,Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA. david.schatz@yale.edu.,Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA.,Howard Hughes Medical Institute, Yale University, New Haven, CT, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA-mediated transposase
A, E
497Helicoverpa zeaMutation(s): 0 
Find proteins for B0F0C5 (Helicoverpa zea)
Go to UniProtKB:  B0F0C5
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*AP*TP*CP*TP*GP*GP*CP*CP*TP*AP*GP*AP*TP*CP*TP*CP*A)-3')B18Helicoverpa zea
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(P*CP*AP*CP*GP*GP*TP*GP*GP*AP*TP*CP*GP*AP*AP*AP*A)-3')C,G16Helicoverpa zea
Entity ID: 4
MoleculeChainsLengthOrganism
DNA (30-MER)D30Helicoverpa zea
Entity ID: 5
MoleculeChainsLengthOrganism
DNA (5'-D(P*TP*TP*TP*TP*CP*GP*AP*TP*C)-3')F9Helicoverpa zea
Entity ID: 6
MoleculeChainsLengthOrganism
DNA (39-MER)H39Helicoverpa zea
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, E
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, E
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.3 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



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 

  • Version 1.0: 2019-10-09
    Type: Initial release
  • Version 1.1: 2019-11-27
    Type: Database references
  • Version 1.2: 2019-12-04
    Type: Database references
  • Version 1.3: 2019-12-18
    Type: Author supporting evidence