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 lifting DNA off the histone octamer at the site of integration ...

    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 H3.3A, E136Homo sapiensMutation(s): 0 
Gene Names: H3F3A, H3.3A, H3F3, PP781, H3F3B, H3.3B, H3-3A, H3-3B
UniProt & NIH Common Fund Data Resources
Find proteins for P84243 (Homo sapiens)
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Go to UniProtKB:  P84243
PHAROS:  P84243
GTEx:  ENSG00000163041 
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UniProt GroupP84243
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4B, F103Homo sapiensMutation(s): 0 
Gene Names: 
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Find proteins for P62805 (Homo sapiens)
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Go to UniProtKB:  P62805
PHAROS:  P62805
GTEx:  ENSG00000274618 ENSG00000197238 ENSG00000197837 ENSG00000158406 ENSG00000278705 ENSG00000197061 ENSG00000270882 ENSG00000270276 ENSG00000273542 ENSG00000277157 ENSG00000276966 ENSG00000276180 ENSG00000278637 ENSG00000275126 
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UniProt GroupP62805
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2A type 1C, G130Homo sapiensMutation(s): 0 
Gene Names: 
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Find proteins for P0C0S8 (Homo sapiens)
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Go to UniProtKB:  P0C0S8
PHAROS:  P0C0S8
GTEx:  ENSG00000196747 ENSG00000196787 ENSG00000278677 ENSG00000276903 
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UniProt GroupP0C0S8
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2B type 1-C/E/F/G/ID, H126Homo sapiensMutation(s): 0 
Gene Names: 
UniProt & NIH Common Fund Data Resources
Find proteins for P62807 (Homo sapiens)
Explore P62807 
Go to UniProtKB:  P62807
PHAROS:  P62807
GTEx:  ENSG00000180596 ENSG00000277224 ENSG00000278588 ENSG00000273802 ENSG00000274290 
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UniProt GroupP62807
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
IntegraseI [auth K],
J [auth L],
K [auth O],
L [auth P]		395Human 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)
UniProt
Find proteins for P14350 (Human spumaretrovirus)
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Go to UniProtKB:  P14350
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UniProt GroupP14350
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Entity ID: 6
MoleculeChainsLengthOrganismImage
DNA (128-MER)M [auth I]128Homo sapiens
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Entity ID: 7
MoleculeChainsLengthOrganismImage
DNA (108-MER)N [auth U]108Homo sapiens
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Entity ID: 8
MoleculeChainsLengthOrganismImage
DNA (33-MER)O [auth T]33Homo sapiens
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Entity ID: 9
MoleculeChainsLengthOrganismImage
DNA (53-MER)P [auth J]53Homo sapiens
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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')R [auth M],
Q		19Pyrobaculum filamentous virus 1
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Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG
Download Ideal Coordinates CCD File 
S [auth K],
T [auth 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

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Entry History & Funding Information

Deposition Data

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

Revision History  (Full details and data files)

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