6PQN | pdb_00006pqn

Crystal structure of HzTransib transposase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.01 Å
  • R-Value Free: 
    0.277 (Depositor), 0.285 (DCC) 
  • R-Value Work: 
    0.219 (Depositor), 0.234 (DCC) 
  • R-Value Observed: 
    0.222 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 6PQN

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 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.

Macromolecule Content 

  • Total Structure Weight: 114.73 kDa 
  • Atom Count: 7,380 
  • Modeled Residue Count: 908 
  • Deposited Residue Count: 994 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative DNA-mediated transposase
A, B
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
Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PO4

Query on PO4



Download:Ideal Coordinates CCD File
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
O [auth B],
P [auth B],
Q [auth B],
R [auth B],
S [auth B]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL

Query on GOL



Download:Ideal Coordinates CCD File
I [auth A],
J [auth A],
K [auth A],
L [auth A],
T [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
C [auth A],
N [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
M [auth B]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.01 Å
  • R-Value Free:  0.277 (Depositor), 0.285 (DCC) 
  • R-Value Work:  0.219 (Depositor), 0.234 (DCC) 
  • R-Value Observed: 0.222 (Depositor) 
Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 160.292α = 90
b = 160.292β = 90
c = 235.858γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
Cootmodel building
XDSdata reduction
XDSdata scaling
AutoSolphasing

Structure Validation

View Full Validation Report



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: 2024-11-06
    Changes: Data collection, Database references, Refinement description, Structure summary