6RNY

PFV intasome - nucleosome strand transfer complex


Experimental Data Snapshot

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

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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: https://doi.org/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. 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.


  • Organizational Affiliation

    Chromatin structure and mobile DNA Laboratory, The Francis Crick Institute, London, NW1 1AT, UK. peter.cherepanov@crick.ac.uk.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3.3
A, E
136Homo sapiensMutation(s): 0 
Gene Names: H3F3AH3.3AH3F3PP781H3F3BH3.3B
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Find proteins for P84243 (Homo sapiens)
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UniProt GroupP84243
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4
B, F
103Homo sapiensMutation(s): 0 
Gene Names: 
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Find proteins for P62805 (Homo sapiens)
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UniProt GroupP62805
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2A type 1
C, G
130Homo sapiensMutation(s): 0 
Gene Names: HIST1H2AGH2AFPHIST1H2AIH2AFCHIST1H2AKH2AFDHIST1H2ALH2AFIHIST1H2AMH2AFN
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Find proteins for P0C0S8 (Homo sapiens)
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B type 1-C/E/F/G/I
D, H
126Homo sapiensMutation(s): 0 
Gene Names: HIST1H2BCH2BFLHIST1H2BEH2BFHHIST1H2BFH2BFGHIST1H2BGH2BFAHIST1H2BIH2BFK
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Find proteins for P62807 (Homo sapiens)
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Entity ID: 5
MoleculeChains Sequence 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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Entity ID: 6
MoleculeChains LengthOrganismImage
DNA (128-MER)M [auth I]128Homo sapiens
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Entity ID: 7
MoleculeChains LengthOrganismImage
DNA (108-MER)N [auth U]108Homo sapiens
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Entity ID: 8
MoleculeChains LengthOrganismImage
DNA (33-MER)O [auth T]33Homo sapiens
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Entity ID: 9
MoleculeChains LengthOrganismImage
DNA (53-MER)P [auth J]53Homo sapiens
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Entity ID: 10
MoleculeChains LengthOrganismImage
DNA (5'-D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP*TP*CP*GP*C)-3')Q,
R [auth M]
19Pyrobaculum filamentous virus 1
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION1.3
MODEL REFINEMENTPHENIX

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