6RNY

PFV intasome - nucleosome strand transfer complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Retroviral integration into nucleosomes through DNA looping and sliding along the histone octamer.

Wilson, M.D.Renault, L.Maskell, D.P.Ghoneim, M.Pye, V.E.Nans, A.Rueda, D.S.Cherepanov, P.Costa, A.

(2019) Nat Commun 10: 4189-4189

  • DOI: 10.1038/s41467-019-12007-w
  • Primary Citation of Related Structures:  
    6R0C, 6RNY

  • PubMed Abstract: 
  • Retroviral integrase can efficiently utilise nucleosomes for insertion of the reverse-transcribed viral DNA. In face of the structural constraints imposed by the nucleosomal structure, integrase gains access to the scissile phosphodiester bonds by liftin ...

    Retroviral integrase can efficiently utilise nucleosomes for insertion of the reverse-transcribed viral DNA. In face of the structural constraints imposed by the nucleosomal structure, integrase gains access to the scissile phosphodiester bonds by lifting DNA off the histone octamer at the site of integration. To clarify the mechanism of DNA looping by integrase, we determined a 3.9 Å resolution structure of the prototype foamy virus intasome engaged with a nucleosome core particle. The structural data along with complementary single-molecule Förster resonance energy transfer measurements reveal twisting and sliding of the nucleosomal DNA arm proximal to the integration site. Sliding the nucleosomal DNA by approximately two base pairs along the histone octamer accommodates the necessary DNA lifting from the histone H2A-H2B subunits to allow engagement with the intasome. Thus, retroviral integration into nucleosomes involves the looping-and-sliding mechanism for nucleosomal DNA repositioning, bearing unexpected similarities to chromatin remodelers.


    Related Citations: 
    • Retroviral integration into nucleosomes through DNA looping and sliding along the histone octamer.
      Wilson, M.D., Renault, L., Maskell, D.P., Ghoneim, M., Pye, V.E., Nans, A., Rueda, D.S., Cherepanov, P., Costa, A.
      (2019) Nat Commun 10: 4189

    Organizational Affiliation

    Macromolecular Machines Laboratory, The Francis Crick Institute, NW1 1AT, London, UK. alessandro.costa@crick.ac.uk.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3.3 AE136Homo sapiensMutation(s): 0 
Gene Names: H3F3AH3.3AH3F3PP781H3F3BH3.3BH3-3AH3-3B
Find proteins for P84243 (Homo sapiens)
Explore P84243 
Go to UniProtKB:  P84243
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PHAROS:  P84243
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4 BF103Homo sapiensMutation(s): 0 
Gene Names: 
Find proteins for P62805 (Homo sapiens)
Explore P62805 
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PHAROS:  P62805
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2A type 1 CG130Homo sapiensMutation(s): 0 
Gene Names: 
Find proteins for P0C0S8 (Homo sapiens)
Explore P0C0S8 
Go to UniProtKB:  P0C0S8
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PHAROS:  P0C0S8
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2B type 1-C/E/F/G/I DH126Homo sapiensMutation(s): 0 
Gene Names: 
Find proteins for P62807 (Homo sapiens)
Explore P62807 
Go to UniProtKB:  P62807
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PHAROS:  P62807
Protein Feature View
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Integrase KLOP395Human spumaretrovirusMutation(s): 2 
Gene Names: pol
EC: 2.7.7.49 (PDB Primary Data), 2.7.7.7 (PDB Primary Data), 3.1.26.4 (PDB Primary Data), 3.4.23 (PDB Primary Data), 2.7.7 (PDB Primary Data), 3.1 (PDB Primary Data)
Find proteins for P14350 (Human spumaretrovirus)
Explore P14350 
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  • Reference Sequence
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Entity ID: 6
MoleculeChainsLengthOrganismImage
DNA (128-MER)I128Homo sapiens
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Entity ID: 7
MoleculeChainsLengthOrganismImage
DNA (108-MER)U108Homo sapiens
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Entity ID: 8
MoleculeChainsLengthOrganismImage
DNA (33-MER)T33Homo sapiens
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Entity ID: 9
MoleculeChainsLengthOrganismImage
DNA (53-MER)J53Homo sapiens
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 10
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP*TP*CP*GP*C)-3')M, Q19Pyrobaculum filamentous virus 1
    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    MG
    Query on MG

    Download Ideal Coordinates CCD File 
    K, O
    MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: ELECTRON MICROSCOPY
    • Resolution: 3.90 Å
    • Aggregation State: PARTICLE 
    • Reconstruction Method: SINGLE PARTICLE 

    Structure Validation

    View Full Validation Report



    Entry History & Funding Information

    Deposition Data


    Funding OrganizationLocationGrant Number
    The Francis Crick InstituteUnited KingdomFC0010061
    The Francis Crick InstituteUnited KingdomFC0010065

    Revision History 

    • Version 1.0: 2019-09-25
      Type: Initial release
    • Version 1.1: 2019-12-18
      Changes: Other