1P3M

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.209 

wwPDB Validation 3D Report Full Report


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: 10.1038/sj.emboj.7600046
  • Primary Citation of Related Structures:  

  • 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 dya ...

    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

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H3
A, E
135Xenopus laevis
Find proteins for P84233 (Xenopus laevis)
Go to UniProtKB:  P84233
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Histone H4
B, F
102Xenopus laevis
Find proteins for P62799 (Xenopus laevis)
Go to UniProtKB:  P62799
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Histone H2A
C, G
129Xenopus laevis
Find proteins for P06897 (Xenopus laevis)
Go to UniProtKB:  P06897
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Histone H2B
D, H
125Xenopus laevis
Find proteins for P02281 (Xenopus laevis)
Go to UniProtKB:  P02281
Entity ID: 1
MoleculeChainsLengthOrganism
Palindromic 146bp Human Alpha-Satellite DNA fragmentI,J146Homo sapiens
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.209 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 105.766α = 90.00
b = 109.634β = 90.00
c = 181.508γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
CNSphasing
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

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