6R0C

Human-D02 Nucleosome Core Particle with biotin-streptavidin label


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 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.


    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: H3F3AH3.3AH3F3PP781H3F3BH3.3BH3-3AH3-3B
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)
Explore P62805 
Go to UniProtKB:  P62805
PHAROS:  P62805
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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)
Explore P0C0S8 
Go to UniProtKB:  P0C0S8
PHAROS:  P0C0S8
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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: 
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Find proteins for P62807 (Homo sapiens)
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PHAROS:  P62807
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UniProt GroupP62807
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Entity ID: 5
MoleculeChainsLengthOrganismImage
DNA (142-MER)I 145Homo sapiens
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Entity ID: 6
MoleculeChainsLengthOrganismImage
DNA (142-MER)J 145Homo sapiens
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Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download Ideal Coordinates CCD File 
K [auth A]MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 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