5NL0

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

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

  • 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: 5.40 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.242 

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
  • Primary Citation of Related Structures:  
    5NL0

  • 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 complex with vertebrate linker histone H1 ...

    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. Electronic address: stefan.dimitrov@univ-grenoble-alpes.fr.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3.2A, E, K135Xenopus laevisMutation(s): 1 
UniProt
Find proteins for P84233 (Xenopus laevis)
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UniProt GroupP84233
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4B, F, L102Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P62799 (Xenopus laevis)
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UniProt GroupP62799
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2A type 1C, G, M129Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P06897 (Xenopus laevis)
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UniProt GroupP06897
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2B 1.1D, H, N122Xenopus laevisMutation(s): 1 
UniProt
Find proteins for P02281 (Xenopus laevis)
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UniProt GroupP02281
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H1.0-BQ [auth Z]196Xenopus laevisMutation(s): 0 
Gene Names: h1f0-b, h1-0-b
UniProt
Find proteins for P22844 (Xenopus laevis)
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Entity ID: 5
MoleculeChainsLengthOrganismImage
DNA (197-MER)I,
O [auth S]		197synthetic construct
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Entity ID: 6
MoleculeChainsLengthOrganismImage
DNA (197-MER)J,
P [auth T]		197synthetic construct
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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 5.40 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.242 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.725α = 90
b = 405.737β = 90
c = 348.162γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
Cootmodel building

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant 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  (Full details and data files)

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