7PEZ

Nucleosome 4 of the 4x177 nucleosome array containing H1

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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Literature

Histone H1 binding to nucleosome arrays depends on linker DNA length and trajectory.

Dombrowski, M., Engeholm, M., Dienemann, C., Dodonova, S., Cramer, P.

(2022) Nat Struct Mol Biol 29: 493-501

  • DOI: 10.1038/s41594-022-00768-w
  • Primary Citation of Related Structures:  
    7PET, 7PEU, 7PEV, 7PEW, 7PEX, 7PEY, 7PEZ, 7PF0, 7PF2, 7PF3, 7PF4, 7PF5, 7PF6, 7PFA, 7PFC, 7PFD, 7PFE, 7PFF, 7PFT, 7PFU, 7PFV, 7PFW, 7PFX

  • PubMed Abstract: 

    • Throughout the genome, nucleosomes often form regular arrays that differ in nucleosome repeat length (NRL), occupancy of linker histone H1 and transcriptional activity. Here, we report cryo-EM structures of human H1-containing tetranucleosome arrays with four physiologically relevant NRLs ...

    Throughout the genome, nucleosomes often form regular arrays that differ in nucleosome repeat length (NRL), occupancy of linker histone H1 and transcriptional activity. Here, we report cryo-EM structures of human H1-containing tetranucleosome arrays with four physiologically relevant NRLs. The structures show a zig-zag arrangement of nucleosomes, with nucleosomes 1 and 3 forming a stack. H1 binding to stacked nucleosomes depends on the NRL, whereas H1 always binds to the non-stacked nucleosomes 2 and 4. Short NRLs lead to altered trajectories of linker DNA, and these altered trajectories sterically impair H1 binding to the stacked nucleosomes in our structures. As the NRL increases, linker DNA trajectories relax, enabling H1 contacts and binding. Our results provide an explanation for why arrays with short NRLs are depleted of H1 and suited for transcription, whereas arrays with long NRLs show full H1 occupancy and can form transcriptionally silent heterochromatin regions.

    Organizational Affiliation: 

    Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany. pcramer@mpinat.mpg.de.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3.2A [auth k],
E [auth o]		136Homo sapiensMutation(s): 1 
Gene Names: HIST2H3A, HIST2H3C, H3F2, H3FM, HIST2H3D, H3C15, H3C14, H3C13
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PHAROS:  Q71DI3
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UniProt GroupQ71DI3
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4B [auth l],
F [auth p]		103Homo sapiensMutation(s): 0 
Gene Names: 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2A type 1-B/EC [auth m],
G [auth q]		147Homo sapiensMutation(s): 0 
Gene Names: H2AC4, H2AFM, HIST1H2AB, H2AC8, H2AFA, HIST1H2AE
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2B type 1-KH [auth e],
D [auth n]		126Homo sapiensMutation(s): 0 
Gene Names: HIST1H2BK, H2BFT, HIRIP1, H2BC12
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H1.4K [auth s]218Homo sapiensMutation(s): 0 
Gene Names: H1-4, H1F4, HIST1H1E
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Entity ID: 5
MoleculeChainsLengthOrganismImage
DNA (182-MER)I [auth J]182synthetic construct
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Entity ID: 6
MoleculeChainsLengthOrganismImage
DNA (182-MER)J [auth I]182synthetic construct
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
European Research Council (ERC)European Union882357

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-03
    Type: Initial release