Biological Assembly 1  

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 48-mer - A12B12C12D12 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Homo 48-mer -A48 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: SAXS

Macromolecule Content

• Total Structure Weight: 1366005.50 
• Atom Count: 82122 
• Residue Count: 8328 
• Unique protein chains: 4
• Unique nucleic acid chains: 2

6HKT

Structure of an H1-bound 6-nucleosome array

• DOI: 10.2210/pdb6HKT/pdb
• NDB: 6HKT

• Classification: DNA BINDING PROTEIN
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2018-09-08 Released: 2018-10-31 
• Deposition Author(s): Garcia-Saez, I., Dimitrov, S., Petosa, C.
• Funding Organization(s): French National Research Agency 

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 9.7 Å
• R-Value Free: 0.286 
• R-Value Work: 0.254 

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

• PubMed: 30392928 
• DOI: 10.1016/j.molcel.2018.09.027


• 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 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.

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Organizational Affiliation: 

Université Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Institute for Advanced Biosciences (IAB), Site Santé - Allée des Alpes, 38700 La Tronche, France; Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS, Laboratoire de Biologie et de Modélisation de la Cellule LBMC, 46 Allée d'Italie, 69007 Lyon, 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. Electronic address: [e-mail].,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: [e-mail].,Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 38000 Grenoble, France.,Université Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Institute for Advanced Biosciences (IAB), Site Santé - Allée des Alpes, 38700 La Tronche, France; Laboratory of the Biology and Pathology of the Eye, Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Albertov 4, 128 00 Prague 2, Czech Republic. Electronic address: [e-mail].,Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 38000 Grenoble, France. Electronic address: [e-mail].,Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS, Laboratoire de Biologie et de Modélisation de la Cellule LBMC, 46 Allée d'Italie, 69007 Lyon, France. Electronic address: [e-mail].

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Histone H3.1	A, E, a, e, K, O, k, o, U, Y, u, y	139	Homo sapiens	Mutation(s): 0  Gene Names: HIST1H3A, HIST1H3B, HIST1H3C, HIST1H3D, HIST1H3E, HIST1H3F, HIST1H3G, HIST1H3H, HIST1H3I, HIST1H3J (H3FA, H3FL, H3FC, H3FB, H3FD, H3FI, H3FH, H3FK, H3FF, H3FJ)
Find proteins for P68431 (Homo sapiens) Go to Gene View: HIST1H3A HIST1H3B HIST1H3C HIST1H3D HIST1H3E HIST1H3F HIST1H3G HIST1H3H HIST1H3I HIST1H3J Go to UniProtKB:  P68431

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Histone H4	B, F, b, f, L, P, l, p, V, Z, v, z	106	Homo sapiens	Mutation(s): 0  Gene Names: HIST1H4A, HIST1H4B, HIST1H4C, HIST1H4D, HIST1H4E, HIST1H4F, HIST1H4H, HIST1H4I, HIST1H4J, HIST1H4K, HIST1H4L, HIST2H4A, HIST2H4B, HIST4H4 (H4/A, H4FA, H4/I, H4FI, H4/G, H4FG, H4/B, H4FB, H4/J, H4FJ, H4/C, H4FC, H4/H, H4FH, H4/M, H4FM, H4/E, H4FE, H4/D, H4FD, H4/K, H4FK, H4/N, H4F2, H4FN, HIST2H4, H4/O, H4FO)
Find proteins for P62805 (Homo sapiens) Go to Gene View: HIST1H4A HIST1H4B HIST1H4C HIST1H4D HIST1H4E HIST1H4F HIST1H4H HIST1H4I HIST1H4J HIST1H4K HIST1H4L HIST2H4A HIST2H4B HIST4H4 Go to UniProtKB:  P62805

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
Histone H2A type 1-B/E	C, G, c, g, M, Q, m, q, W, 0, w, 2	133	Homo sapiens	Mutation(s): 0  Gene Names: HIST1H2AB, HIST1H2AE (H2AFM, H2AFA)
Find proteins for P04908 (Homo sapiens) Go to Gene View: HIST1H2AB HIST1H2AE Go to UniProtKB:  P04908

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
Histone H2B type 1-J	D, H, d, h, N, R, n, r, X, 1, x, 3	129	Homo sapiens	Mutation(s): 0  Gene Names: HIST1H2BJ (H2BFR)
Find proteins for P06899 (Homo sapiens) Go to Gene View: HIST1H2BJ Go to UniProtKB:  P06899

Entity ID: 5
Molecule	Chains	Length	Organism
DNA (1122-MER)	I	1122	synthetic construct

Entity ID: 6
Molecule	Chains	Length	Organism
DNA (1122-MER)	J	1122	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 9.7 Å
• R-Value Free: 0.286 
• R-Value Work: 0.254 
• Space Group: P 2 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 111.078	α = 90.00
b = 238.761	β = 90.00
c = 674.368	γ = 90.00

Software Package:

Software Name	Purpose
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
XDS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2018-09-08 
• Released Date: 2018-10-31 
• Deposition Author(s): Garcia-Saez, I., Dimitrov, S., Petosa, C.

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Funding Organization	Location	Grant Number
French National Research Agency	France	ANR-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
  Type: Data collection, Database references
• Version 1.2: 2018-12-19
  Type: Data collection, Database references