6R0C

Human-D02 Nucleosome Core Particle with biotin-streptavidin label


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.2 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.0 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:  
  • Also Cited By: 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 li ...

    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.,Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, EH9 3JR, UK.,Chromatin structure and mobile DNA Laboratory, The Francis Crick Institute, London, NW1 1AT, UK.,Faculty of Biological Sciences, Leeds, LS2 9JT, UK.,Structural Biology Science Technology Platform, The Francis Crick Institute, London, NW1 1AT, UK.,Single Molecule Imaging Group, MRC London Institute for Medical Science, London, W12 0NN, UK. david.rueda@imperial.ac.uk.,Molecular Virology, Department of Medicine, Imperial College London, London, W12 0NN, UK.,Single Molecule Imaging Group, MRC London Institute for Medical Science, London, W12 0NN, UK.,Molecular Virology, Department of Medicine, Imperial College London, London, W12 0NN, UK. david.rueda@imperial.ac.uk.,Department of Medicine, Imperial College London, St-Mary's Campus, Norfolk Place, London, W2 1PG, UK. peter.cherepanov@crick.ac.uk.,Macromolecular Machines Laboratory, The Francis Crick Institute, NW1 1AT, London, UK.,NeCEN, University of Leiden, 2333CC, Leiden, Netherlands.,Macromolecular Machines Laboratory, The Francis Crick Institute, NW1 1AT, London, UK. alessandro.costa@crick.ac.uk.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone H3.3
A, E
136Homo sapiensMutation(s): 0 
Gene Names: H3-3A, H3-3B (H3.3A, H3F3, H3F3A, H3.3B, H3F3B)
Find proteins for P84243 (Homo sapiens)
Go to UniProtKB:  P84243
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H4
B, F
103Homo sapiensMutation(s): 0 
Gene Names: H4C1, H4C2, H4C3, H4C4, H4C5, H4C6, H4C8, H4C9, H4C11, H4C12, H4C13, H4C14, H4C15, H4-16 (H4/A, H4FA, HIST1H4A, H4/I, H4FI, HIST1H4B, H4/G, H4FG, HIST1H4C, H4/B, H4FB, HIST1H4D, H4/J, H4FJ, HIST1H4E, H4/C, H4FC, HIST1H4F, H4/H, H4FH, HIST1H4H, H4/M, H4FM, HIST1H4I, H4/E, H4FE, HIST1H4J, H4/D, H4FD, HIST1H4K, H4/K, H4FK, HIST1H4L, H4/N, H4F2, H4FN, HIST2H4, HIST2H4A, H4/O, H4FO, HIST2H4B, HIST4H4)
Find proteins for P62805 (Homo sapiens)
Go to UniProtKB:  P62805
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Histone H2A type 1
C, G
130Homo sapiensMutation(s): 0 
Gene Names: H2AC11, H2AC13, H2AC15, H2AC16, H2AC17 (H2AFP, HIST1H2AG, H2AFC, HIST1H2AI, H2AFD, HIST1H2AK, H2AFI, HIST1H2AL, H2AFN, HIST1H2AM)
Find proteins for P0C0S8 (Homo sapiens)
Go to UniProtKB:  P0C0S8
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Histone H2B type 1-C/E/F/G/I
D, H
126Homo sapiensMutation(s): 0 
Gene Names: H2BC4, H2BC6, H2BC7, H2BC8, H2BC10 (H2BFL, HIST1H2BC, H2BFH, HIST1H2BE, H2BFG, HIST1H2BF, H2BFA, HIST1H2BG, H2BFK, HIST1H2BI)
Find proteins for P62807 (Homo sapiens)
Go to UniProtKB:  P62807
Entity ID: 5
MoleculeChainsLengthOrganism
DNA (142-MER)I145Homo sapiens
Entity ID: 6
MoleculeChainsLengthOrganism
DNA (142-MER)J145Homo sapiens
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.2 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



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