Structure of the HTLV-2 integrase catalytic core domain in complex with magnesium (dimeric form)

Experimental Data Snapshot

  • Resolution: 2.45 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.233 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


Cryo-EM structure of the deltaretroviral intasome in complex with the PP2A regulatory subunit B56 gamma.

Barski, M.S.Minnell, J.J.Hodakova, Z.Pye, V.E.Nans, A.Cherepanov, P.Maertens, G.N.

(2020) Nat Commun 11: 5043-5043

  • DOI: https://doi.org/10.1038/s41467-020-18874-y
  • Primary Citation of Related Structures:  
    6QBT, 6QBV, 6QBW, 6TJU, 6TOQ, 7PEL

  • PubMed Abstract: 

    Human T-cell lymphotropic virus type 1 (HTLV-1) is a deltaretrovirus and the most oncogenic pathogen. Many of the ~20 million HTLV-1 infected people will develop severe leukaemia or an ALS-like motor disease, unless a therapy becomes available. A key step in the establishment of infection is the integration of viral genetic material into the host genome, catalysed by the retroviral integrase (IN) enzyme. Here, we use X-ray crystallography and single-particle cryo-electron microscopy to determine the structure of the functional deltaretroviral IN assembled on viral DNA ends and bound to the B56γ subunit of its human host factor, protein phosphatase 2 A. The structure reveals a tetrameric IN assembly bound to two molecules of the phosphatase via a conserved short linear motif. Insight into the deltaretroviral intasome and its interaction with the host will be crucial for understanding the pattern of integration events in infected individuals and therefore bears important clinical implications.

  • Organizational Affiliation

    Imperial College London, St Mary's Hospital, Department of Infectious Disease, Section of Virology, Norfolk Place, London, W2 1PG, UK.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D
164Human T-lymphotropic virus 2Mutation(s): 0 
Gene Names: pol
Find proteins for P03363 (Human T-cell leukemia virus 2)
Explore P03363 
Go to UniProtKB:  P03363
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03363
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.45 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.233 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 185.315α = 90
b = 89.175β = 102.485
c = 65.53γ = 90
Software Package:
Software NamePurpose
Cootmodel building
xia2data reduction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom107005

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-30
    Type: Initial release
  • Version 1.1: 2021-04-14
    Changes: Database references
  • Version 1.2: 2024-05-15
    Changes: Data collection, Database references