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
  • Structures With Same Primary Citation

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



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone H3.2
A, E, K
135Xenopus laevisMutation(s): 1 
Find proteins for P84233 (Xenopus laevis)
Go to UniProtKB:  P84233
Protein Feature View
  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H4
B, F, L
102Xenopus laevisMutation(s): 0 
Find proteins for P62799 (Xenopus laevis)
Go to UniProtKB:  P62799
Protein Feature View
  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Histone H2A type 1
C, G, M
129Xenopus laevisMutation(s): 0 
Find proteins for P06897 (Xenopus laevis)
Go to UniProtKB:  P06897
Protein Feature View
  • Reference Sequence

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Histone H2B 1.1
D, H, N
122Xenopus laevisMutation(s): 1 
Find proteins for P02281 (Xenopus laevis)
Go to UniProtKB:  P02281
Protein Feature View
  • Reference Sequence

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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Histone H1.0-B
Z
196Xenopus laevisMutation(s): 0 
Gene Names: h1f0-b, h1-0-b
Find proteins for P22844 (Xenopus laevis)
Go to UniProtKB:  P22844
Protein Feature View
  • Reference Sequence

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Entity ID: 5
MoleculeChainsLengthOrganism
DNA (197-MER)I, S197synthetic construct

Find similar nucleic acids by: Sequence  |  Structure

Entity ID: 6
MoleculeChainsLengthOrganism
DNA (197-MER)J, T197synthetic construct
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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View more in-depth experimental data

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 

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