6LA9

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


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 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


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

  • DOI: https://doi.org/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.


  • Organizational Affiliation

    School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3.1
A, E, K, O
136Homo sapiensMutation(s): 0 
Gene Names: 
UniProt & NIH Common Fund Data Resources
Find proteins for P68431 (Homo sapiens)
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PHAROS:  P68431
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UniProt GroupP68431
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4
B, F, L, P
103Homo sapiensMutation(s): 0 
Gene Names: 
UniProt & NIH Common Fund Data Resources
Find proteins for P62805 (Homo sapiens)
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PHAROS:  P62805
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UniProt GroupP62805
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2A type 1-B/E
C, G, M, Q
130Homo sapiensMutation(s): 0 
Gene Names: HIST1H2ABH2AFMHIST1H2AEH2AFA
UniProt & NIH Common Fund Data Resources
Find proteins for P04908 (Homo sapiens)
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PHAROS:  P04908
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UniProt GroupP04908
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B type 1-J
D, H, N, R
126Homo sapiensMutation(s): 0 
Gene Names: HIST1H2BJH2BFR
UniProt & NIH Common Fund Data Resources
Find proteins for P06899 (Homo sapiens)
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PHAROS:  P06899
GTEx:  ENSG00000124635 
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UniProt GroupP06899
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H1.0
S, T
194Homo sapiensMutation(s): 0 
Gene Names: H1-0H1F0H1FV
UniProt & NIH Common Fund Data Resources
Find proteins for P07305 (Homo sapiens)
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PHAROS:  P07305
GTEx:  ENSG00000189060 
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Entity ID: 5
MoleculeChains LengthOrganismImage
DNA (349-MER)349other sequences
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Entity ID: 6
MoleculeChains LengthOrganismImage
DNA (349-MER)349other sequences
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download Ideal Coordinates CCD File 
AA [auth I]
AB [auth J]
BA [auth I]
BB [auth J]
CA [auth I]
AA [auth I],
AB [auth J],
BA [auth I],
BB [auth J],
CA [auth I],
CB [auth J],
DA [auth I],
DB [auth J],
EA [auth I],
FA [auth I],
FB [auth O],
GA [auth I],
GB [auth O],
HA [auth I],
HB [auth O],
IA [auth I],
IB [auth O],
JA [auth I],
JB [auth Q],
KA [auth I],
LA [auth I],
MA [auth I],
NA [auth I],
PA [auth J],
QA [auth J],
RA [auth J],
SA [auth J],
TA [auth J],
U [auth A],
UA [auth J],
V [auth C],
VA [auth J],
W [auth F],
WA [auth J],
X [auth G],
XA [auth J],
Y [auth G],
YA [auth J],
Z [auth I],
ZA [auth J]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
EB [auth J],
OA [auth I]
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 = 120.78α = 90
b = 172.88β = 90
c = 216.041γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education (Singapore)Singapore--

Revision History  (Full details and data files)

  • Version 1.0: 2020-10-07
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description