4BAC

prototype foamy virus strand transfer complexes on product DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.263 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1002/pro.2166

  • 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 subs ...

    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

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
INTEGRASE
A, B
396Human spumaretrovirusGene Names: pol
EC: 3.1.26.4, 3.1.-.-, 2.7.7.49, 2.7.7.7, 2.7.7.-, 3.4.23.-
Find proteins for P14350 (Human spumaretrovirus)
Go to UniProtKB:  P14350
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP *TP*TP*GP*TP*AP)-3'C19synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (38-MER)D38synthetic construct
Entity ID: 4
MoleculeChainsLengthOrganism
5'-D(*AP*GP*GP*AP*GP*CP*CP*AP*AP*GP*AP*CP*GP*GP *AP*TP*CP)-3'E17synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.263 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.185 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 160.617α = 90.00
b = 160.617β = 90.00
c = 125.092γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
PHENIXrefinement
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-10-10
    Type: Initial release
  • Version 1.1: 2012-12-12
    Type: Database references, Other, Structure summary