3LEL

Structural Insight into the Sequence-Dependence of Nucleosome Positioning


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.229 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural insight into the sequence dependence of nucleosome positioning

Wu, B.Mohideen, K.Vasudevan, D.Davey, C.A.

(2010) Structure 18: 528-536

  • DOI: 10.1016/j.str.2010.01.015

  • PubMed Abstract: 
  • Nucleosome positioning displays sequence dependency and contributes to genomic regulation in a site-specific manner. We solved the structures of nucleosome core particle composed of strong positioning TTTAA elements flanking the nucleosome center. Th ...

    Nucleosome positioning displays sequence dependency and contributes to genomic regulation in a site-specific manner. We solved the structures of nucleosome core particle composed of strong positioning TTTAA elements flanking the nucleosome center. The positioning strength of the super flexible TA dinucleotide is consistent with its observed central location within minor groove inward regions, where it can contribute maximally to energetically challenging minor groove bending, kinking and compression. The marked preference for TTTAA and positioning power of the site 1.5 double helix turns from the nucleosome center relates to a unique histone protein motif at this location, which enforces a sustained, extremely narrow minor groove via a hydrophobic "sugar clamp." Our analysis sheds light on the basis of nucleosome positioning and indicates that the histone octamer has evolved not to fully minimize sequence discrimination in DNA binding.


    Organizational Affiliation

    Division of Structural and Computational Biology, School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone H3.2
A, E, K, O
136Xenopus laevis
Find proteins for P84233 (Xenopus laevis)
Go to UniProtKB:  P84233
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H4
B, F, L, P
102Xenopus laevis
Find proteins for P62799 (Xenopus laevis)
Go to UniProtKB:  P62799
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Histone H2A
C, G, M, Q
128Xenopus laevisGene Names: hist1h2aj (LOC494591)
Find proteins for Q6AZJ8 (Xenopus laevis)
Go to UniProtKB:  Q6AZJ8
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Histone H2B 1.1
D, H, N, R
125Xenopus laevis
Find proteins for P02281 (Xenopus laevis)
Go to UniProtKB:  P02281
Entity ID: 5
MoleculeChainsLengthOrganism
147-MER DNAI,S147N/A
Entity ID: 6
MoleculeChainsLengthOrganism
147-MER DNAJ,T147N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
G, I, J, N, O, S, T
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.229 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 106.747α = 90.00
b = 178.508β = 102.78
c = 110.412γ = 90.00
Software Package:
Software NamePurpose
MAR345dtbdata collection
SCALAdata scaling
REFMACrefinement
AMoREphasing
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-05-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance