5MLU

Crystal structure of the PFV GAG CBS bound to a mononucleosome


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.209 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis for spumavirus GAG tethering to chromatin.

Lesbats, P.Serrao, E.Maskell, D.P.Pye, V.E.O'Reilly, N.Lindemann, D.Engelman, A.N.Cherepanov, P.

(2017) Proc Natl Acad Sci U S A 114: 5509-5514

  • DOI: 10.1073/pnas.1621159114
  • Primary Citation of Related Structures:  
    5MLU

  • PubMed Abstract: 
  • The interactions between a retrovirus and host cell chromatin that underlie integration and provirus expression are poorly understood. The prototype foamy virus (PFV) structural protein GAG associates with chromosomes via a chromatin-binding sequence (CBS) located within its C-terminal region ...

    The interactions between a retrovirus and host cell chromatin that underlie integration and provirus expression are poorly understood. The prototype foamy virus (PFV) structural protein GAG associates with chromosomes via a chromatin-binding sequence (CBS) located within its C-terminal region. Here, we show that the PFV CBS is essential and sufficient for a direct interaction with nucleosomes and present a crystal structure of the CBS bound to a mononucleosome. The CBS interacts with the histone octamer, engaging the H2A-H2B acidic patch in a manner similar to other acidic patch-binding proteins such as herpesvirus latency-associated nuclear antigen (LANA). Substitutions of the invariant arginine anchor residue in GAG result in global redistribution of PFV and macaque simian foamy virus (SFV mac ) integration sites toward centromeres, dampening the resulting proviral expression without affecting the overall efficiency of integration. Our findings underscore the importance of retroviral structural proteins for integration site selection and the avoidance of genomic junkyards.


    Organizational Affiliation

    Division of Medicine, Imperial College London W2 1PG, United Kingdom.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3.2A, E97Xenopus laevisMutation(s): 1 
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Find proteins for P84233 (Xenopus laevis)
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UniProt GroupP84233
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4B, F84Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P62799 (Xenopus laevis)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2A type 1C, G105Xenopus laevisMutation(s): 1 
UniProt
Find proteins for P06897 (Xenopus laevis)
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UniProt GroupP06897
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2BD93Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P02281 (Xenopus laevis)
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UniProt GroupP02281
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2BH94Xenopus laevisMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
PFV GAG peptideI [auth M]17Simian foamy virusMutation(s): 0 
UniProt
Find proteins for P14349 (Human spumaretrovirus)
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Entity ID: 7
MoleculeChainsLengthOrganismImage
DNA (145-MER)J [auth I]145Escherichia coli
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Entity ID: 8
MoleculeChainsLengthOrganismImage
DNA (145-MER)K [auth J]145Escherichia coli
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Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.209 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.26α = 90
b = 109.45β = 90
c = 175.82γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-10
    Type: Initial release
  • Version 1.1: 2017-05-24
    Changes: Database references
  • Version 1.2: 2017-05-31
    Changes: Database references