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 
  • R-Value Observed: 0.231 

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
  • Primary Citation of Related Structures:  
    3LEL

  • 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. 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 ...

    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

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3.2A, E, K, O136Xenopus 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, F, L, P102Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P62799 (Xenopus laevis)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2AC, G, M, Q128Xenopus laevisMutation(s): 0 
Gene Names: h2ac14.Lh2ac14hist1h2ajLOC494591XELAEV_18003602mg
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Find proteins for Q6AZJ8 (Xenopus laevis)
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UniProt GroupQ6AZJ8
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2B 1.1D, H, N, R125Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P02281 (Xenopus laevis)
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Go to UniProtKB:  P02281
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UniProt GroupP02281
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Entity ID: 5
MoleculeChainsLengthOrganismImage
147-MER DNAI, S 147N/A
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Entity ID: 6
MoleculeChainsLengthOrganismImage
147-MER DNAJ, T 147N/A
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Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download Ideal Coordinates CCD File 
AA [auth I],
AB [auth T],
BA [auth J],
BB [auth T],
CA [auth J],
AA [auth I],
AB [auth T],
BA [auth J],
BB [auth T],
CA [auth J],
DA [auth J],
EA [auth J],
FA [auth J],
GA [auth J],
HA [auth J],
IA [auth J],
JA [auth N],
KA [auth O],
LA [auth S],
MA [auth S],
NA [auth S],
OA [auth S],
PA [auth S],
QA [auth S],
RA [auth S],
SA [auth S],
TA [auth T],
U [auth G],
UA [auth T],
V [auth I],
VA [auth T],
W [auth I],
WA [auth T],
X [auth I],
XA [auth T],
Y [auth I],
YA [auth T],
Z [auth I],
ZA [auth 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 
  • R-Value Observed: 0.231 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.747α = 90
b = 178.508β = 102.78
c = 110.412γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
AMoREphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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