Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 18-mer - A4B4C4D4E2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 18-mer - A9B7C2 

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

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content

• Total Structure Weight: 478.83 kDa 
• Atom Count: 27560 
• Residue Count: 2365 
• Unique protein chains: 5
• Unique nucleic acid chains: 2

6LA9

349 bp di-nucleosome harboring cohesive DNA termini assembled with linker histone H1.0 (high cryoprotectant)

• DOI: 10.2210/pdb6LA9/pdb
• NDB: 6LA9

• Classification: DNA BINDING PROTEIN
• Organism(s): Homo sapiens, other sequences
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-11-12 Released: 2020-10-07 
• Deposition Author(s): Adhireksan, Z., Sharma, D., Lee, P.L., Davey, C.A.
• Funding Organization(s): Ministry of Education (Singapore)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.70 Å
• R-Value Free: 0.266 
• R-Value Work: 0.194 
• R-Value Observed: 0.196 

Literature

Near-atomic resolution structures of interdigitated nucleosome fibres.

Adhireksan, Z., Sharma, D., Lee, P.L., Davey, C.A.

(2020) Nat Commun 11: 4747-4747

• PubMed: 32958761 
• DOI: 10.1038/s41467-020-18533-2
• Primary Citation of Related Structures:  
  6LA8, 6LA9, 6M3V, 6M44


• PubMed Abstract: 
  

Chromosome structure at the multi-nucleosomal level has remained ambiguous in spite of its central role in epigenetic regulation and genome dynamics. Recent investigations of chromatin architecture portray diverse modes of interaction within and between nucleosome chains, but how this is realized at the atomic level is unclear. Here we present near-atomic resolution crystal structures of nucleosome fibres that assemble from cohesive-ended dinucleosomes with and without linker histone. As opposed to adopting folded helical '30 nm' structures, the fibres instead assume open zigzag conformations that are interdigitated with one another. Zigzag conformations obviate extreme bending of the linker DNA, while linker DNA size (nucleosome repeat length) dictates fibre configuration and thus fibre-fibre packing, which is supported by variable linker histone binding. This suggests that nucleosome chains have a predisposition to interdigitate with specific characteristics under condensing conditions, which rationalizes observations of local chromosome architecture and the general heterogeneity of chromatin structure.

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Organizational Affiliation: 

NTU Institute of Structural Biology, Nanyang Technological University, 59 Nanyang Drive, Singapore, 636921, Singapore. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.1	A, E, K, O	136	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) Explore P68431  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	Image
Histone H4	B, F, L, P	103	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) Explore P62805  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: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A type 1-B/E	C, G, M, Q	130	Homo sapiens	Mutation(s): 0  Gene Names: HIST1H2AB, H2AFM, HIST1H2AE, H2AFA, H2AC4, H2AC8
Find proteins for P04908 (Homo sapiens) Explore P04908  Go to UniProtKB:  P04908
NIH Common Fund Data Resources
PHAROS  P04908 GTEx  ENSG00000277075GTEx  ENSG00000278463

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B type 1-J	D, H, N, R	126	Homo sapiens	Mutation(s): 0  Gene Names: HIST1H2BJ, H2BFR, H2BC11
Find proteins for P06899 (Homo sapiens) Explore P06899  Go to UniProtKB:  P06899
NIH Common Fund Data Resources
PHAROS  P06899 GTEx  ENSG00000124635

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H1.0	S, T	194	Homo sapiens	Mutation(s): 0  Gene Names: H1-0, H1F0, H1FV
Find proteins for P07305 (Homo sapiens) Explore P07305  Go to UniProtKB:  P07305
NIH Common Fund Data Resources
PHAROS  P07305 GTEx  ENSG00000189060

Entity ID: 5
Molecule	Chains	Length	Organism	Image
DNA (349-MER)	I	349	other sequences

Entity ID: 6
Molecule	Chains	Length	Organism	Image
DNA (349-MER)	J	349	other sequences

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	A, C, F, G, I, J, O, Q	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
K	I, J	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.70 Å
• R-Value Free: 0.266 
• R-Value Work: 0.194 
• R-Value Observed: 0.196 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.78	α = 90
b = 172.88	β = 90
c = 216.041	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2019-11-12 
• Released Date: 2020-10-07 
Deposition Author(s): Adhireksan, Z., Sharma, D., Lee, P.L., Davey, C.A.

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Funding Organization	Location	Grant Number
Ministry of Education (Singapore)	Singapore	--

Revision History 

• Version 1.0: 2020-10-07
  Type: Initial release