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 1.0 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: 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 ...

    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: 

    NTU Institute of Structural Biology, Nanyang Technological University, 59 Nanyang Drive, Singapore, 636921, Singapore. davey@ntu.edu.sg.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3.1A, E, K, O136Homo sapiensMutation(s): 0 
Gene Names: 
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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
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4B, F, L, P103Homo sapiensMutation(s): 0 
Gene Names: 
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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
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2A type 1-B/EC, G, M, Q130Homo sapiensMutation(s): 0 
Gene Names: HIST1H2AB, H2AFM, HIST1H2AE, H2AFA, H2AC4, H2AC8
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Find proteins for P04908 (Homo sapiens)
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PHAROS:  P04908
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2B type 1-JD, H, N, R126Homo sapiensMutation(s): 0 
Gene Names: HIST1H2BJ, H2BFR, H2BC11
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Find proteins for P06899 (Homo sapiens)
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PHAROS:  P06899
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H1.0S, T194Homo sapiensMutation(s): 0 
Gene Names: H1-0, H1F0, H1FV
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Find proteins for P07305 (Homo sapiens)
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PHAROS:  P07305
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Entity ID: 5
MoleculeChainsLengthOrganismImage
DNA (349-MER)I349other sequences
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Entity ID: 6
MoleculeChainsLengthOrganismImage
DNA (349-MER)J349other sequences
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Small Molecules
Ligands 2 Unique
IDChainsName / 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		 Ligand Interaction
K
Query on K
Download Ideal Coordinates CCD File 
EB [auth J],
OA [auth I]		POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N		 Ligand Interaction
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