5NL0

Crystal structure of a 197-bp palindromic 601L nucleosome in complex with linker histone H1

  • Classification: CHROMATIN BINDING PROTEIN / DNA
  • Organism(s): synthetic construct, Xenopus laevis
  • Expression System: Escherichia coli
  • Mutation(s): 

  • Deposited: 2017-04-03 Released: 2017-05-17 
  • Deposition Author(s): Garcia-Saez, I., Petosa, C., Dimitrov, S.
  • Funding Organization(s): Fondation pour la Recherche Medicale. Programme Epigenetique et Stabilite du Genome; Association pour la Recherche sur le Cancer; French National Research Agency; French Infrastructure for Integrated Structural Biology (FRISBI); FRISBI; Labex GRAL (Grenoble Alliance for Integrated Structural Cell Biology) 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 5.4 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.240 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure and Dynamics of a 197 bp Nucleosome in Complex with Linker Histone H1.

Bednar, J.Garcia-Saez, I.Boopathi, R.Cutter, A.R.Papai, G.Reymer, A.Syed, S.H.Lone, I.N.Tonchev, O.Crucifix, C.Menoni, H.Papin, C.Skoufias, D.A.Kurumizaka, H.Lavery, R.Hamiche, A.Hayes, J.J.Schultz, P.Angelov, D.Petosa, C.Dimitrov, S.

(2017) Mol. Cell 66: 384-397.e8

  • DOI: 10.1016/j.molcel.2017.04.012

  • PubMed Abstract: 
  • Linker histones associate with nucleosomes to promote the formation of higher-order chromatin structure, but the underlying molecular details are unclear. We investigated the structure of a 197 bp nucleosome bearing symmetric 25 bp linker DNA arms in ...

    Linker histones associate with nucleosomes to promote the formation of higher-order chromatin structure, but the underlying molecular details are unclear. We investigated the structure of a 197 bp nucleosome bearing symmetric 25 bp linker DNA arms in complex with vertebrate linker histone H1. We determined electron cryo-microscopy (cryo-EM) and crystal structures of unbound and H1-bound nucleosomes and validated these structures by site-directed protein cross-linking and hydroxyl radical footprinting experiments. Histone H1 shifts the conformational landscape of the nucleosome by drawing the two linkers together and reducing their flexibility. The H1 C-terminal domain (CTD) localizes primarily to a single linker, while the H1 globular domain contacts the nucleosome dyad and both linkers, associating more closely with the CTD-distal linker. These findings reveal that H1 imparts a strong degree of asymmetry to the nucleosome, which is likely to influence the assembly and architecture of higher-order structures.


    Organizational Affiliation

    Institut for Advanced Biosciences, Inserm U 1209, CNRS UMR 5309, Université Grenoble Alpes, 38000 Grenoble, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone H3.2
A, E, K
135Xenopus laevisMutations: G102A
Find proteins for P84233 (Xenopus laevis)
Go to UniProtKB:  P84233
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H4
B, F, L
102Xenopus laevis
Find proteins for P62799 (Xenopus laevis)
Go to UniProtKB:  P62799
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Histone H2A type 1
C, G, M
129Xenopus laevis
Find proteins for P06897 (Xenopus laevis)
Go to UniProtKB:  P06897
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Histone H2B 1.1
D, H, N
122Xenopus laevisMutations: S29T
Find proteins for P02281 (Xenopus laevis)
Go to UniProtKB:  P02281
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Histone H1.0-B
Z
196Xenopus laevisGene Names: h1f0-b
Find proteins for P22844 (Xenopus laevis)
Go to UniProtKB:  P22844
Entity ID: 5
MoleculeChainsLengthOrganism
DNA (197-MER)I,S197synthetic construct
Entity ID: 6
MoleculeChainsLengthOrganism
DNA (197-MER)J,T197synthetic construct
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 5.4 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.240 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 61.725α = 90.00
b = 405.737β = 90.00
c = 348.162γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Cootmodel building
PHASERphasing
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
Fondation pour la Recherche Medicale. Programme Epigenetique et Stabilite du GenomeFrance--
Association pour la Recherche sur le CancerFranceChromcomp grant
French National Research AgencyFranceChrome grant
French Infrastructure for Integrated Structural Biology (FRISBI)FranceANR-10-INSB-05-01
FRISBIFranceANR-10-INSB-05-02
Labex GRAL (Grenoble Alliance for Integrated Structural Cell Biology)FranceANR-10-LABX-49-01

Revision History 

  • Version 1.0: 2017-05-17
    Type: Initial release
  • Version 1.1: 2017-08-30
    Type: Author supporting evidence