4BAC

prototype foamy virus strand transfer complexes on product DNA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.26 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 

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This is version 1.3 of the entry. See complete history. 


Literature

Assembly of Prototype Foamy Virus Strand Transfer Complexes on Product DNA Bypassing Catalysis of Integration.

Yin, Z., Lapkouski, M., Yang, W., Craigie, R.

(2012) Protein Sci 21: 1849

  • DOI: https://doi.org/10.1002/pro.2166
  • Primary Citation of Related Structures:  
    4BAC

  • PubMed Abstract: 

    Integrase is the key enzyme that mediates integration of retroviral DNA into cellular DNA which is essential for viral replication. Inhibitors of HIV-1 that target integrase recognize the nucleoprotein complexes formed by integrase and viral DNA substrate (intasomes) rather than the free enzyme. Atomic resolution structures of HIV-1 intasomes are therefore required to understand the mechanisms of inhibition and drug resistance. To date, prototype foamy virus (PFV) is the only retrovirus for which such structures have been determined. We show that PFV strand transfer complexes (STC) can be assembled on product DNA without going through the normal forward reaction pathway. The finding that a retroviral STC can be assembled in this way may provide a powerful tool to alleviate the obstacles that impede structural studies of nucleoprotein intermediates in HIV-1 DNA integration.

    • Organizational Affiliation: 

    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
INTEGRASE
A, B
396Human spumaretrovirusMutation(s): 0 
EC: 2.7.7.49 (PDB Primary Data), 2.7.7.7 (PDB Primary Data), 3.1.26.13 (PDB Primary Data)
UniProt
Find proteins for P14350 (Human spumaretrovirus)
Explore P14350 
Go to UniProtKB:  P14350
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14350
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
5'-D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP *TP*TP*GP*TP*AP)-3'19synthetic construct
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (38-MER)38synthetic construct
Sequence Annotations
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  • Reference Sequence

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Entity ID: 4
MoleculeChains LengthOrganismImage
5'-D(*AP*GP*GP*AP*GP*CP*CP*AP*AP*GP*AP*CP*GP*GP *AP*TP*CP)-3'17synthetic construct
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.26 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 160.617α = 90
b = 160.617β = 90
c = 125.092γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-10-10
    Type: Initial release
  • Version 1.1: 2012-12-12
    Changes: Database references, Other, Structure summary
  • Version 1.2: 2019-05-08
    Changes: Data collection, Experimental preparation, Other
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description