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): 2 

  • 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.,Department of Integrated Structural Biology, Institut de Génétique et Biologie Moléculaire et Cellulaire (IGBMC)/Université de Strasbourg/CNRS/INSERM, 67404 Illkirch Cedex, France. Electronic address: patrick.schultz@igbmc.fr.,Université de Lyon, Institut NeuroMyoGène (INMG) CNRS/UCBL UMR5310 & Laboratoire de Biologie et de Modélisation de la Cellule (LBMC) CNRS/ENSL/UCBL, Ecole Normale Supérieure de Lyon, 69007 Lyon, France. Electronic address: dimitar.anguelov@ens-lyon.fr.,Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France. Electronic address: carlo.petosa@ibs.fr.,Institut for Advanced Biosciences, Inserm U 1209, CNRS UMR 5309, Université Grenoble Alpes, 38000 Grenoble, France. Electronic address: stefan.dimitrov@univ-grenoble-alpes.fr.,MMSB, University of Lyon I/CNRS UMR 5086, Institut de Biologie et Chimie des Protéines, 69367 Lyon, France.,Department of Biochemistry and Biophysics, University of Rochester, Rochester, New York 14642, USA. Electronic address: jeffrey_hayes@URMC.rochester.edu.,Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France.,Department of Integrated Structural Biology, Institut de Génétique et Biologie Moléculaire et Cellulaire (IGBMC)/Université de Strasbourg/CNRS/INSERM, 67404 Illkirch Cedex, France.,Département de Génomique Fonctionnelle et Cancer, Institut de Génétique et Biologie Moléculaire et Cellulaire (IGBMC)/Université de Strasbourg/CNRS/INSERM, 67404 Illkirch Cedex, France.,Institut for Advanced Biosciences, Inserm U 1209, CNRS UMR 5309, Université Grenoble Alpes, 38000 Grenoble, France; Université de Lyon, Institut NeuroMyoGène (INMG) CNRS/UCBL UMR5310 & Laboratoire de Biologie et de Modélisation de la Cellule (LBMC) CNRS/ENSL/UCBL, Ecole Normale Supérieure de Lyon, 69007 Lyon, France.,Department of Biochemistry and Biophysics, University of Rochester, Rochester, New York 14642, USA.,Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan.,Département de Génomique Fonctionnelle et Cancer, Institut de Génétique et Biologie Moléculaire et Cellulaire (IGBMC)/Université de Strasbourg/CNRS/INSERM, 67404 Illkirch Cedex, France. Electronic address: hamiche@igbmc.fr.




Macromolecules

Find similar proteins by: Sequence  |  Structure


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
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H4
B, F, L
102Xenopus laevisMutation(s): 0 
Find proteins for P62799 (Xenopus laevis)
Go to UniProtKB:  P62799
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
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
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Histone H1.0-B
Z
196Xenopus laevisMutation(s): 0 
Gene Names: h1-0-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


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
    Type: Author supporting evidence