7PEL

CryoEM structure of simian T-cell lymphotropic virus intasome in complex with PP2A regulatory subunit B56 gamma


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.34 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
View more details

wwPDB Validation   3D Report Full Report


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 B56gamma.

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

(2020) Nat Commun 11: 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,
B,
F [auth D],
G [auth E]
301Simian T-lymphotropic virus 1Mutation(s): 0 
Gene Names: pol
UniProt
Find proteins for Q4QY51 (Simian T-lymphotropic virus 1)
Explore Q4QY51 
Go to UniProtKB:  Q4QY51
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4QY51
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform 3 of PC4 and SFRS1-interacting protein,Isoform Gamma-2 of Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoformC,
H [auth F]
697Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for O75475 (Homo sapiens)
Explore O75475 
Go to UniProtKB:  O75475
PHAROS:  O75475
GTEx:  ENSG00000164985 
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 GroupsQ13362O75475
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(*AP*CP*TP*GP*TP*GP*TP*TP*TP*GP*GP*CP*GP*CP*TP*TP*CP*TP*CP*TP*C)-3')D [auth K],
I [auth M]
30synthetic construct
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains LengthOrganismImage
DNA (5'-D(*GP*AP*GP*AP*GP*AP*AP*GP*CP*GP*CP*CP*AP*AP*AP*CP*AP*CP*A)-3')E [auth L],
J [auth N]
28synthetic construct
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.34 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.18-3845
MODEL REFINEMENTCoot0.8.9.2
RECONSTRUCTIONRELION3.1

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom107005/Z/15Z
Royal SocietyUnited KingdomRG120032
Cancer Research UKUnited KingdomFC001061
Medical Research Council (MRC, United Kingdom)United KingdomFC001061
Wellcome TrustUnited KingdomFC001061

Revision History  (Full details and data files)

  • Version 1.0: 2021-08-25
    Type: Initial release
  • Version 1.1: 2024-07-10
    Changes: Data collection, Database references, Refinement description