6HKT

Structure of an H1-bound 6-nucleosome array


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 9.70 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.254 
  • R-Value Observed: 0.255 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of an H1-Bound 6-Nucleosome Array Reveals an Untwisted Two-Start Chromatin Fiber Conformation.

Garcia-Saez, I.Menoni, H.Boopathi, R.Shukla, M.S.Soueidan, L.Noirclerc-Savoye, M.Le Roy, A.Skoufias, D.A.Bednar, J.Hamiche, A.Angelov, D.Petosa, C.Dimitrov, S.

(2018) Mol Cell 72: 902-915.e7

  • DOI: 10.1016/j.molcel.2018.09.027
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Chromatin adopts a diversity of regular and irregular fiber structures in vitro and in vivo. However, how an array of nucleosomes folds into and switches between different fiber conformations is poorly understood. We report the 9.7 Å resolution cryst ...

    Chromatin adopts a diversity of regular and irregular fiber structures in vitro and in vivo. However, how an array of nucleosomes folds into and switches between different fiber conformations is poorly understood. We report the 9.7 Å resolution crystal structure of a 6-nucleosome array bound to linker histone H1 determined under ionic conditions that favor incomplete chromatin condensation. The structure reveals a flat two-start helix with uniform nucleosomal stacking interfaces and a nucleosome packing density that is only half that of a twisted 30-nm fiber. Hydroxyl radical footprinting indicates that H1 binds the array in an on-dyad configuration resembling that observed for mononucleosomes. Biophysical, cryo-EM, and crosslinking data validate the crystal structure and reveal that a minor change in ionic environment shifts the conformational landscape to a more compact, twisted form. These findings provide insights into the structural plasticity of chromatin and suggest a possible assembly pathway for a 30-nm fiber.


    Organizational Affiliation

    Université Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Institute for Advanced Biosciences (IAB), Site Santé - Allée des Alpes, 38700 La Tronche, France; "Roumen Tsanev" Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia, Bulgaria. Electronic address: stefan.dimitrov@univ-grenoble-alpes.fr.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone H3.1
A, E, K, O, U, Y, a, e, k, o, u, y
139Homo sapiensMutation(s): 0 
Gene Names: 
Find proteins for P68431 (Homo sapiens)
Go to UniProtKB:  P68431
NIH Common Fund Data Resources
PHAROS  P68431

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H4
B, F, L, P, V, Z, b, f, l, p, v, z
106Homo sapiensMutation(s): 0 
Gene Names: 
Find proteins for P62805 (Homo sapiens)
Go to UniProtKB:  P62805
NIH Common Fund Data Resources
PHAROS  P62805

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Histone H2A type 1-B/E
0, 2, C, G, M, Q, W, c, g, m, q, w
133Homo sapiensMutation(s): 0 
Gene Names: HIST1H2ABH2AFMHIST1H2AEH2AFAH2AC4H2AC8
Find proteins for P04908 (Homo sapiens)
Go to UniProtKB:  P04908
NIH Common Fund Data Resources
PHAROS  P04908

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Histone H2B type 1-J
1, 3, D, H, N, R, X, d, h, n, r, x
129Homo sapiensMutation(s): 0 
Gene Names: HIST1H2BJH2BFRH2BC11
Find proteins for P06899 (Homo sapiens)
Go to UniProtKB:  P06899
NIH Common Fund Data Resources
PHAROS  P06899

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Entity ID: 5
MoleculeChainsLengthOrganism
DNA (1122-MER)I1122synthetic construct

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Entity ID: 6
MoleculeChainsLengthOrganism
DNA (1122-MER)J1122synthetic construct
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 9.70 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.254 
  • R-Value Observed: 0.255 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.078α = 90
b = 238.761β = 90
c = 674.368γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Research AgencyFranceANR-10-LABX-0030, ANR-12-BSV5-0017, ANR-14-CE09-0019, ANR-16- CE12-0013, ANR-17-CE11-0019, ANR-18-CE12-0010

Revision History 

  • Version 1.0: 2018-10-31
    Type: Initial release
  • Version 1.1: 2018-11-14
    Changes: Data collection, Database references
  • Version 1.2: 2018-12-19
    Changes: Data collection, Database references