6FQ5

Class 1 : canonical nucleosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.8 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural rearrangements of the histone octamer translocate DNA.

Bilokapic, S.Strauss, M.Halic, M.

(2018) Nat Commun 9: 1330-1330

  • DOI: 10.1038/s41467-018-03677-z
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Nucleosomes, the basic unit of chromatin, package and regulate expression of eukaryotic genomes. Nucleosomes are highly dynamic and are remodeled with the help of ATP-dependent remodeling factors. Yet, the mechanism of DNA translocation around the hi ...

    Nucleosomes, the basic unit of chromatin, package and regulate expression of eukaryotic genomes. Nucleosomes are highly dynamic and are remodeled with the help of ATP-dependent remodeling factors. Yet, the mechanism of DNA translocation around the histone octamer is poorly understood. In this study, we present several nucleosome structures showing histone proteins and DNA in different organizational states. We observe that the histone octamer undergoes conformational changes that distort the overall nucleosome structure. As such, rearrangements in the histone core α-helices and DNA induce strain that distorts and moves DNA at SHL 2. Distortion of the nucleosome structure detaches histone α-helices from the DNA, leading to their rearrangement and DNA translocation. Biochemical assays show that cross-linked histone octamers are immobilized on DNA, indicating that structural changes in the octamer move DNA. This intrinsic plasticity of the nucleosome is exploited by chromatin remodelers and might be used by other chromatin machineries.


    Organizational Affiliation

    Gene Ceter, Department of Biochemistry, University of Munich LMU, 81377, Munich, Germany.,Cryo EM Facility, Max Planck Institute for Biochemistry, 82152, Martinsried, Germany.,Gene Ceter, Department of Biochemistry, University of Munich LMU, 81377, Munich, Germany. halic@genzentrum.lmu.de.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
histone H3
A, E
98Xenopus laevisMutation(s): 0 
Find proteins for P84233 (Xenopus laevis)
Go to UniProtKB:  P84233
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H4
B
84Xenopus laevisMutation(s): 0 
Find proteins for P62799 (Xenopus laevis)
Go to UniProtKB:  P62799
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Histone H2A
C, G
110Xenopus laevisMutation(s): 0 
Find proteins for P06897 (Xenopus laevis)
Go to UniProtKB:  P06897
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Histone H2B
D, H
95Xenopus laevisMutation(s): 0 
Find proteins for P02281 (Xenopus laevis)
Go to UniProtKB:  P02281
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Histone H4
F
85Xenopus laevisMutation(s): 0 
Find proteins for P62799 (Xenopus laevis)
Go to UniProtKB:  P62799
Entity ID: 6
MoleculeChainsLengthOrganism
DNA (147-MER)I147synthetic construct
Entity ID: 7
MoleculeChainsLengthOrganism
DNA (147-MER)J147synthetic construct
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.8 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research CouncilERC-smallRNAhet-309584

Revision History 

  • Version 1.0: 2018-04-18
    Type: Initial release
  • Version 1.1: 2019-10-23
    Type: Data collection, Other