6TOQ

Crystal structure of a PP2A B56y/HTLV-1 integrase complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.16 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.227 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pol proteinA [auth CCC]98Human T-cell leukemia virus type IMutation(s): 0 
Gene Names: pol
UniProt
Find proteins for A0A1Y1CAL3 (Human T-cell leukemia virus type I)
Explore A0A1Y1CAL3 
Go to UniProtKB:  A0A1Y1CAL3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1Y1CAL3
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoformB [auth AAA]370Homo sapiensMutation(s): 0 
Gene Names: PPP2R5CKIAA0044
UniProt & NIH Common Fund Data Resources
Find proteins for Q13362 (Homo sapiens)
Explore Q13362 
Go to UniProtKB:  Q13362
PHAROS:  Q13362
GTEx:  ENSG00000078304 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13362
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.16 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.227 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.77α = 90
b = 58.77β = 90
c = 321.15γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Cootmodel building
xia2data reduction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom107005

Revision History  (Full details and data files)

  • Version 1.0: 2020-10-21
    Type: Initial release
  • Version 1.1: 2024-01-24
    Changes: Data collection, Database references, Derived calculations, Refinement description