6LA2

343 bp di-nucleosome harboring cohesive DNA termini assembled with linker histone H1.0

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.89 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Engineering nucleosomes for generating diverse chromatin assemblies.

Adhireksan, Z., Sharma, D., Lee, P.L., Bao, Q., Padavattan, S., Shum, W.K., Davey, G.E., Davey, C.A.

(2021) Nucleic Acids Res 49: e52-e52

  • DOI: https://doi.org/10.1093/nar/gkab070
  • Primary Citation of Related Structures:  
    6L9Z, 6LA2, 6LAB, 6LER, 7COW

  • PubMed Abstract: 

    • Structural characterization of chromatin is challenging due to conformational and compositional heterogeneity in vivo and dynamic properties that limit achievable resolution in vitro. Although the maximum resolution for solving structures of large macromolecular assemblies by electron microscopy has recently undergone profound increases, X-ray crystallographic approaches may still offer advantages for certain systems ...

    Structural characterization of chromatin is challenging due to conformational and compositional heterogeneity in vivo and dynamic properties that limit achievable resolution in vitro. Although the maximum resolution for solving structures of large macromolecular assemblies by electron microscopy has recently undergone profound increases, X-ray crystallographic approaches may still offer advantages for certain systems. One such system is compact chromatin, wherein the crystalline state recapitulates the crowded molecular environment within the nucleus. Here we show that nucleosomal constructs with cohesive-ended DNA can be designed that assemble into different types of circular configurations or continuous fibers extending throughout crystals. We demonstrate the utility of the method for characterizing nucleosome compaction and linker histone binding at near-atomic resolution but also advance its application for tackling further problems in chromatin structural biology and for generating novel types of DNA nanostructures. We provide a library of cohesive-ended DNA fragment expression constructs and a strategy for engineering DNA-based nanomaterials with a seemingly vast potential variety of architectures and histone chemistries.

    Organizational Affiliation: 

    NTU Institute of Structural Biology, Nanyang Technological University, 59 Nanyang Drive, 636921, Singapore.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3.1136Homo sapiensMutation(s): 0 
Gene Names: 
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UniProt GroupP68431
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4103Homo sapiensMutation(s): 0 
Gene Names: 
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Find proteins for P62805 (Homo sapiens)
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UniProt GroupP62805
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2A type 1-B/E130Homo 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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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2B type 1-J126Homo sapiensMutation(s): 0 
Gene Names: HIST1H2BJ, H2BFR, H2BC11
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Find proteins for P06899 (Homo sapiens)
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H1.0
S, T
194Homo sapiensMutation(s): 0 
Gene Names: H1-0, H1F0, H1FV
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Find proteins for P07305 (Homo sapiens)
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UniProt GroupP07305
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Entity ID: 5
MoleculeChainsLengthOrganismImage
DNA (343-MER)CA [auth c],
I		343other sequences
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Entity ID: 6
MoleculeChainsLengthOrganismImage
DNA (343-MER)DA [auth d],
J		343other sequences
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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.89 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.755α = 90
b = 205.904β = 97.19
c = 237.677γ = 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: 2021-02-17
    Type: Initial release
  • Version 1.1: 2021-08-18
    Changes: Database references