1P3A

Crystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.203 

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This is version 1.2 of the entry. See complete history. 


Literature

Crystal structures of histone Sin mutant nucleosomes reveal altered protein-DNA interactions

Muthurajan, U.M., Bao, Y., Forsberg, L.J., Edayathumangalam, R.S., Dyer, P.N., White, C.L., Luger, K.

(2004) EMBO J 23: 260-271

  • DOI: https://doi.org/10.1038/sj.emboj.7600046
  • Primary Citation of Related Structures:  
    1P34, 1P3A, 1P3B, 1P3F, 1P3G, 1P3I, 1P3K, 1P3L, 1P3M, 1P3O, 1P3P

  • PubMed Abstract: 

    • Here we describe 11 crystal structures of nucleosome core particles containing individual point mutations in the structured regions of histones H3 and H4. The mutated residues are located at the two protein-DNA interfaces flanking the nucleosomal dyad. Five of the mutations partially restore the in vivo effects of SWI/SNF inactivation in yeast ...

    Here we describe 11 crystal structures of nucleosome core particles containing individual point mutations in the structured regions of histones H3 and H4. The mutated residues are located at the two protein-DNA interfaces flanking the nucleosomal dyad. Five of the mutations partially restore the in vivo effects of SWI/SNF inactivation in yeast. We find that even nonconservative mutations of these residues (which exhibit a distinct phenotype in vivo) have only moderate effects on global nucleosome structure. Rather, local protein-DNA interactions are disrupted and weakened in a subtle and complex manner. The number of lost protein-DNA interactions correlates directly with an increased propensity of the histone octamer to reposition with respect to the DNA, and with an overall destabilization of the nucleosome. Thus, the disruption of only two to six of the approximately 120 direct histone-DNA interactions within the nucleosome has a pronounced effect on nucleosome mobility and stability. This has implications for our understanding of how these structures are made accessible to the transcription and replication machinery in vivo.

    Organizational Affiliation: 

    Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3C [auth A],
G [auth E]		135Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P84233 (Xenopus laevis)
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UniProt GroupP84233
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4D [auth B],
H [auth F]		102Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P62799 (Xenopus laevis)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2AE [auth C],
I [auth G]		129Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P06897 (Xenopus laevis)
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UniProt GroupP06897
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2BF [auth D],
J [auth H]		125Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P02281 (Xenopus laevis)
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UniProt GroupP02281
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Entity ID: 1
MoleculeChainsLengthOrganismImage
Palindromic 146bp Human Alpha-Satellite DNA fragmentA [auth I],
B [auth J]		146Homo sapiens
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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.203 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.423α = 90
b = 109.721β = 90
c = 180.902γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-02-24
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance