5F99

X-ray Structure of the MMTV-A Nucleosome Core Particle

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.63 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.175 

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Literature

X-ray structure of the MMTV-A nucleosome core.

Frouws, T.D., Duda, S.C., Richmond, T.J.

(2016) Proc Natl Acad Sci U S A 113: 1214-1219

  • DOI: 10.1073/pnas.1524607113
  • Primary Citation of Related Structures:  
    5F99

  • PubMed Abstract: 

    • The conformation of DNA bound in nucleosomes depends on the DNA sequence. Questions such as how nucleosomes are positioned and how they potentially bind sequence-dependent nuclear factors require near-atomic resolution structures of the nucleosome core containing different DNA sequences; despite this, only the DNA for two similar α-satellite sequences and a sequence (601) selected in vitro have been visualized bound in the nucleosome core ...

    The conformation of DNA bound in nucleosomes depends on the DNA sequence. Questions such as how nucleosomes are positioned and how they potentially bind sequence-dependent nuclear factors require near-atomic resolution structures of the nucleosome core containing different DNA sequences; despite this, only the DNA for two similar α-satellite sequences and a sequence (601) selected in vitro have been visualized bound in the nucleosome core. Here we report the 2.6-Å resolution X-ray structure of a nucleosome core particle containing the DNA sequence of nucleosome A of the 3'-LTR of the mouse mammary tumor virus (147 bp MMTV-A). To our knowledge, this is the first nucleosome core particle structure containing a promoter sequence and crystallized from Mg(2+) ions. It reveals sequence-dependent DNA conformations not seen previously, including kinking into the DNA major groove.

    Organizational Affiliation: 

    Institute of Molecular Biology and Biophysics, Department of Biology, Swiss Federal Institute of Technology Zurich, 8093 Zurich, Switzerland richmond@mol.biol.ethz.ch.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3.2A, E135Xenopus laevisMutation(s): 0 
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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, F103Xenopus laevisMutation(s): 1 
UniProt
Find proteins for P62799 (Xenopus laevis)
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UniProt GroupP62799
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2A type 1C, G129Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P06897 (Xenopus laevis)
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UniProt GroupP06897
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2B 1.1D, H122Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P02281 (Xenopus laevis)
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UniProt GroupP02281
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Entity ID: 5
MoleculeChainsLengthOrganismImage
DNA (147-MER)I 147Mouse mammary tumor virus
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Entity ID: 6
MoleculeChainsLengthOrganismImage
DNA (147-MER)J 147Mouse mammary tumor virus
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Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.63 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.175 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.873α = 90
b = 178.915β = 90
c = 109.061γ = 90
Software Package:
Software NamePurpose
CNSrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-02-03
    Type: Initial release
  • Version 1.1: 2016-02-10
    Changes: Database references