5OY7

Structure of the 4_601_157 tetranucleosome (P1 form)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 5.774 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.219 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Capturing Structural Heterogeneity in Chromatin Fibers.

Ekundayo, B.Richmond, T.J.Schalch, T.

(2017) J. Mol. Biol. 429: 3031-3042

  • DOI: 10.1016/j.jmb.2017.09.002
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Chromatin fiber organization is implicated in processes such as transcription, DNA repair and chromosome segregation, but how nucleosomes interact to form higher-order structure remains poorly understood. We solved two crystal structures of tetranucl ...

    Chromatin fiber organization is implicated in processes such as transcription, DNA repair and chromosome segregation, but how nucleosomes interact to form higher-order structure remains poorly understood. We solved two crystal structures of tetranucleosomes with approximately 11-bp DNA linker length at 5.8 and 6.7 Å resolution. Minimal intramolecular nucleosome-nucleosome interactions result in a fiber model resembling a flat ribbon that is compatible with a two-start helical architecture, and that exposes histone and DNA surfaces to the environment. The differences in the two structures combined with electron microscopy reveal heterogeneous structural states, and we used site-specific chemical crosslinking to assess the diversity of nucleosome-nucleosome interactions through identification of structure-sensitive crosslink sites that provide a means to characterize fibers in solution. The chromatin fiber architectures observed here provide a basis for understanding heterogeneous chromatin higher-order structures as they occur in a genomic context.


    Organizational Affiliation

    Department of Molecular Biology, Faculty of Sciences, University of Geneva, CH-1211 Geneva 4, Switzerland; Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, CH-1211 Geneva 4, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone H2B 1.1
L, P, D, H, T, X, b, f
126Xenopus laevisMutation(s): 0 
Find proteins for P02281 (Xenopus laevis)
Go to UniProtKB:  P02281
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H3
M, Q, I, A, E, U, Y, c
135Xenopus laevisMutation(s): 0 
Find proteins for P84233 (Xenopus laevis)
Go to UniProtKB:  P84233
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Histone H4
N, R, J, B, F, V, Z, d
102Xenopus laevisMutation(s): 0 
Find proteins for P62799 (Xenopus laevis)
Go to UniProtKB:  P62799
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Histone H2A
O, C, G, K, S, W, a, e
130Xenopus laevisMutation(s): 0 
Find proteins for P06897 (Xenopus laevis)
Go to UniProtKB:  P06897
Entity ID: 5
MoleculeChainsLengthOrganism
DNA (619-MER)g634synthetic construct
Entity ID: 6
MoleculeChainsLengthOrganism
DNA (619-MER)h628synthetic construct
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
a, C, e, G, K, O, S, W
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 5.774 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.219 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 66.624α = 78.94
b = 161.465β = 83.86
c = 227.915γ = 83.74
Software Package:
Software NamePurpose
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerlandP00P3-139137
Swiss National Science FoundationSwitzerlandPP00P3_163760
Swiss National Science FoundationSwitzerlandPP00P3_172904
European Research CouncilSwitzerlandGrant FP/2007-2013/Agreement 322778

Revision History 

  • Version 1.0: 2017-09-20
    Type: Initial release
  • Version 1.1: 2017-10-18
    Type: Database references