8OOA

CryoEM Structure INO80core Hexasome complex Hexasome refinement state1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.18 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 8OOA


Literature

Hexasome-INO80 complex reveals structural basis of noncanonical nucleosome remodeling.

Zhang, M.Jungblut, A.Kunert, F.Hauptmann, L.Hoffmann, T.Kolesnikova, O.Metzner, F.Moldt, M.Weis, F.DiMaio, F.Hopfner, K.P.Eustermann, S.

(2023) Science 381: 313-319

  • DOI: https://doi.org/10.1126/science.adf6287
  • Primary Citation of Related Structures:  
    8OO7, 8OO9, 8OOA, 8OOC, 8OOF, 8OOK, 8OOP, 8OOR, 8OOS, 8OOT

  • PubMed Abstract: 

    Loss of H2A-H2B histone dimers is a hallmark of actively transcribed genes, but how the cellular machinery functions in the context of noncanonical nucleosomal particles remains largely elusive. In this work, we report the structural mechanism for adenosine 5'-triphosphate-dependent chromatin remodeling of hexasomes by the INO80 complex. We show how INO80 recognizes noncanonical DNA and histone features of hexasomes that emerge from the loss of H2A-H2B. A large structural rearrangement switches the catalytic core of INO80 into a distinct, spin-rotated mode of remodeling while its nuclear actin module remains tethered to long stretches of unwrapped linker DNA. Direct sensing of an exposed H3-H4 histone interface activates INO80, independently of the H2A-H2B acidic patch. Our findings reveal how the loss of H2A-H2B grants remodelers access to a different, yet unexplored layer of energy-driven chromatin regulation.


  • Organizational Affiliation

    Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.


Macromolecules

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3.1C [auth M],
G [auth Q]
135Homo sapiensMutation(s): 0 
Gene Names: 
UniProt & NIH Common Fund Data Resources
Find proteins for P68431 (Homo sapiens)
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Go to UniProtKB:  P68431
PHAROS:  P68431
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UniProt GroupP68431
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4D [auth N],
H [auth R]
102Homo sapiensMutation(s): 0 
Gene Names: 
UniProt & NIH Common Fund Data Resources
Find proteins for P62805 (Homo sapiens)
Explore P62805 
Go to UniProtKB:  P62805
PHAROS:  P62805
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UniProt GroupP62805
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2AE [auth O]129Homo sapiensMutation(s): 0 
Gene Names: H2AC6H2AFLHIST1H2AC
UniProt & NIH Common Fund Data Resources
Find proteins for Q93077 (Homo sapiens)
Explore Q93077 
Go to UniProtKB:  Q93077
PHAROS:  Q93077
GTEx:  ENSG00000180573 
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UniProt GroupQ93077
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  • Reference Sequence
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2BF [auth P]125Homo sapiensMutation(s): 0 
Gene Names: HIST1H2BCH2BFLHIST1H2BEH2BFHHIST1H2BFH2BFGHIST1H2BGH2BFAHIST1H2BIH2BFK
UniProt & NIH Common Fund Data Resources
Find proteins for P62807 (Homo sapiens)
Explore P62807 
Go to UniProtKB:  P62807
PHAROS:  P62807
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UniProt GroupP62807
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  • Reference Sequence
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Entity ID: 1
MoleculeChains LengthOrganismImage
DNA strand 1A [auth K]226synthetic construct
Sequence Annotations
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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA Strand 2B [auth L]226synthetic construct
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.18 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1
RECONSTRUCTIONRELION4

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
EIPOD fellowship under Marie Sklodowska-Curie Actions COFUNDGermany847543
European Research Council (ERC)European Union833613
German Research Foundation (DFG)GermanyCRC136
German Research Foundation (DFG)GermanyCRC1064

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-26
    Type: Initial release
  • Version 1.1: 2023-08-02
    Changes: Database references
  • Version 1.2: 2024-07-24
    Changes: Data collection, Refinement description