9J8M

Cryo-EM structure of BAF-Lamin A/C IgF-nucleosome complex (High mobility complex)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.82 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Cryo-EM structures of the BAF-Lamin A/C complex bound to nucleosomes.

Horikoshi, N.Miyake, R.Sogawa-Fujiwara, C.Ogasawara, M.Takizawa, Y.Kurumizaka, H.

(2025) Nat Commun 16: 1495-1495

  • DOI: https://doi.org/10.1038/s41467-025-56823-9
  • Primary Citation of Related Structures:  
    9J8M, 9J8N, 9J8O

  • PubMed Abstract: 

    Barrier-to-autointegration factor (BAF) associates with mitotic chromosomes and promotes nuclear envelope assembly by recruiting proteins, such as Lamins, required for the reconstruction of the nuclear envelope and lamina. BAF also mediates chromatin anchoring to the nuclear lamina via Lamin A/C. However, the mechanism by which BAF and Lamin A/C bind chromatin and affect the chromatin organization remains elusive. Here we report the cryo-electron microscopy structures of BAF-Lamin A/C-nucleosome complexes. We find that the BAF dimer complexed with the Lamin A/C IgF domain occupies the nucleosomal dyad position, forming a tripartite nucleosomal DNA binding structure. We also show that the Lamin A/C Lys486 and His506 residues, which are reportedly mutated in lipodystrophy patients, directly contact the DNA at the nucleosomal dyad. Excess BAF-Lamin A/C complexes symmetrically bind other nucleosomal DNA sites and connect two BAF-Lamin A/C-nucleosome complexes. Although the linker histone H1 competes with BAF-Lamin A/C binding at the nucleosomal dyad region, the two BAF-Lamin A/C molecules still bridge two nucleosomes. These findings provide insights into the mechanism by which BAF, Lamin A/C, and/or histone H1 bind nucleosomes and influence chromatin organization within the nucleus.


  • Organizational Affiliation

    Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, Japan.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3.1
A, E
139Homo 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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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4
B, F
106Homo sapiensMutation(s): 0 
Gene Names: H4C1
UniProt & NIH Common Fund Data Resources
Find proteins for P62805 (Homo sapiens)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2A type 1-B/E
C, G
133Homo sapiensMutation(s): 0 
Gene Names: H2AC4H2AFMHIST1H2ABH2AC8H2AFAHIST1H2AE
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PHAROS:  P04908
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B type 1-J
D, H
129Homo sapiensMutation(s): 0 
Gene Names: H2BC11H2BFRHIST1H2BJ
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GTEx:  ENSG00000124635 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Barrier-to-autointegration factor
K, L
93Homo sapiensMutation(s): 0 
Gene Names: BANF1BAFBCRG1
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Find proteins for O75531 (Homo sapiens)
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PHAROS:  O75531
GTEx:  ENSG00000175334 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Lamin-A/C158Homo sapiensMutation(s): 0 
Gene Names: LMNALMN1
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PHAROS:  P02545
GTEx:  ENSG00000160789 
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.82 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)JapanJP22K06076
Japan Society for the Promotion of Science (JSPS)JapanJP23K24013
Japan Society for the Promotion of Science (JSPS)JapanJP24H02328
Japan Society for the Promotion of Science (JSPS)JapanJP22K06098
Japan Society for the Promotion of Science (JSPS)JapanJP24H02319
Japan Society for the Promotion of Science (JSPS)JapanJP24H02328
Japan Society for the Promotion of Science (JSPS)JapanJP23H05475
Japan Science and TechnologyJapanJPMJER1901
Japan Agency for Medical Research and Development (AMED)JapanJP24ama121009
Japan Agency for Medical Research and Development (AMED)JapanJP24ama121002

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-26
    Type: Initial release