Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 48-mer - A12BCD Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 48-mer - A42B6 

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

Biological Assembly Evidence: SAXS

Macromolecule Content

• Total Structure Weight: 1366.01 kDa 
• Atom Count: 82122 
• Residue Count: 6792 
• 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)
• Mutation(s): No 


• 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

---

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 

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
• 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 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: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Histone H3.1	A, E, K, O, U, Y, a, e, k, o, u, y	139	Homo sapiens	Mutation(s): 0  Gene Names:  HIST1H3A, H3FA, HIST1H3B, H3FL, HIST1H3C, H3FC, HIST1H3D, H3FB, HIST1H3E, H3FD, HIST1H3F, H3FI, HIST1H3G, H3FH, HIST1H3H, H3FK, HIST1H3I, H3FF, HIST1H3J, H3FJ, H3C1, H3C2, H3C3, H3FC HIST1H3C, H3C4, H3C6, H3C7, H3C8, H3C10, H3C11, H3C12
Find proteins for P68431 (Homo sapiens) Go to UniProtKB:  P68431
NIH Common Fund Data Resources
PHAROS  P68431 GTEx  ENSG00000197409GTEx  ENSG00000197153GTEx  ENSG00000278828GTEx  ENSG00000275714GTEx  ENSG00000273983GTEx  ENSG00000274750GTEx  ENSG00000275379GTEx  ENSG00000277775

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Histone H4	B, F, L, P, V, Z, b, f, l, p, v, z	106	Homo sapiens	Mutation(s): 0  Gene Names:  HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, H4FE, HIST1H4K, H4/D, H4FD, HIST1H4L, H4/K, H4FK, HIST2H4A, H4/N, H4F2, H4FN, HIST2H4, HIST2H4B, H4/O, H4FO, HIST4H4, H4C1, H4C2, H4C3, H4C4, H4C5, H4C6, H4C8, H4C9, H4C11, H4C12, H4C13, H4C14, H4C15, H4-16
Find proteins for P62805 (Homo sapiens) Go to UniProtKB:  P62805
NIH Common Fund Data Resources
PHAROS  P62805 GTEx  ENSG00000274618GTEx  ENSG00000197238GTEx  ENSG00000197837GTEx  ENSG00000158406GTEx  ENSG00000278705GTEx  ENSG00000197061GTEx  ENSG00000270882GTEx  ENSG00000270276GTEx  ENSG00000273542GTEx  ENSG00000277157GTEx  ENSG00000276966GTEx  ENSG00000276180GTEx  ENSG00000278637GTEx  ENSG00000275126

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
Histone H2B type 1-J	1, 3, D, H, N, R, X, d, h, n, r, x	129	Homo sapiens	Mutation(s): 0  Gene Names: HIST1H2BJ, H2BFR, H2BC11
Find proteins for P06899 (Homo sapiens) Go to UniProtKB:  P06899
NIH Common Fund Data Resources
PHAROS  P06899 GTEx  ENSG00000124635

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
Histone H2A type 1-B/E	0, 2, C, G, M, Q, W, c, g, m, q, w	133	Homo sapiens	Mutation(s): 0  Gene Names: HIST1H2AB, H2AFM, HIST1H2AE, H2AFA, H2AC4, H2AC8
Find proteins for P04908 (Homo sapiens) Go to UniProtKB:  P04908
NIH Common Fund Data Resources
PHAROS  P04908 GTEx  ENSG00000277075GTEx  ENSG00000278463

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: 9.70 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 = 111.078	α = 90
b = 238.761	β = 90
c = 674.368	γ = 90

Software Package:

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

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.

---

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
  Changes: Data collection, Database references
• Version 1.2: 2018-12-19
  Changes: Data collection, Database references