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- EMDB-61233: Cryo-EM structure of BAF-Lamin A/C IgF-H1-nucleosome complex -

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Basic information

Entry
Database: EMDB / ID: EMD-61233
TitleCryo-EM structure of BAF-Lamin A/C IgF-H1-nucleosome complex
Map data
Sample
  • Complex: Complex containing BAF, Lamin A/C IgF, H1, and nucleosome
    • Protein or peptide: Histone H3.1
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A type 1-B/E
    • Protein or peptide: Histone H2B type 1-J
    • DNA: DNA (193-MER)
    • DNA: DNA (193-MER)
    • Protein or peptide: Barrier-to-autointegration factor
    • Protein or peptide: Lamin-A/C
    • Protein or peptide: Histone H1.1
KeywordsNucleosome / DNA binding proteins / Nuclear lamina / NUCLEAR PROTEIN
Function / homology
Function and homology information


negative regulation of mesenchymal cell proliferation / structural constituent of nuclear lamina / negative regulation of protein ADP-ribosylation / ventricular cardiac muscle cell development / establishment or maintenance of microtubule cytoskeleton polarity / Breakdown of the nuclear lamina / DNA double-strand break attachment to nuclear envelope / Depolymerization of the Nuclear Lamina / nuclear envelope organization / nuclear pore localization ...negative regulation of mesenchymal cell proliferation / structural constituent of nuclear lamina / negative regulation of protein ADP-ribosylation / ventricular cardiac muscle cell development / establishment or maintenance of microtubule cytoskeleton polarity / Breakdown of the nuclear lamina / DNA double-strand break attachment to nuclear envelope / Depolymerization of the Nuclear Lamina / nuclear envelope organization / nuclear pore localization / Nuclear Envelope Breakdown / lamin filament / protein localization to nuclear envelope / mitotic nuclear membrane reassembly / XBP1(S) activates chaperone genes / negative regulation of DNA recombination / nuclear lamina / Apoptosis induced DNA fragmentation / Initiation of Nuclear Envelope (NE) Reformation / regulation of protein localization to nucleus / chromosome condensation / regulation of telomere maintenance / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / intermediate filament / negative regulation of cardiac muscle hypertrophy in response to stress / nucleosomal DNA binding / nuclear migration / negative regulation of type I interferon production / negative regulation of viral genome replication / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / muscle organ development / negative regulation of cGAS/STING signaling pathway / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / 2-LTR circle formation / Vpr-mediated nuclear import of PICs / negative regulation of release of cytochrome c from mitochondria / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / negative regulation of tumor necrosis factor-mediated signaling pathway / protein localization to nucleus / chromosome organization / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / condensed chromosome / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Deposition of new CENPA-containing nucleosomes at the centromere / telomere organization / Inhibition of DNA recombination at telomere / Meiotic synapsis / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / innate immune response in mucosa / negative regulation of innate immune response / SUMOylation of chromatin organization proteins / DNA methylation / Condensation of Prophase Chromosomes / regulation of cell migration / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / SIRT1 negatively regulates rRNA expression / epigenetic regulation of gene expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / negative regulation of extrinsic apoptotic signaling pathway / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / lipopolysaccharide binding / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / euchromatin / G2/M DNA damage checkpoint / HDMs demethylate histones / NoRC negatively regulates rRNA expression / regulation of protein stability / response to virus / DNA Damage/Telomere Stress Induced Senescence / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / DNA integration / Meiotic recombination / chromatin DNA binding / Pre-NOTCH Transcription and Translation / structural constituent of cytoskeleton / positive regulation of receptor-mediated endocytosis
Similarity search - Function
Barrier- to-autointegration factor, BAF / Barrier-to-autointegration factor, BAF superfamily / : / Barrier to autointegration factor / Barrier to autointegration factor / Lamin tail domain superfamily / Lamin tail domain / Lamin Tail Domain / Lamin-tail (LTD) domain profile. / Intermediate filament protein, conserved site ...Barrier- to-autointegration factor, BAF / Barrier-to-autointegration factor, BAF superfamily / : / Barrier to autointegration factor / Barrier to autointegration factor / Lamin tail domain superfamily / Lamin tail domain / Lamin Tail Domain / Lamin-tail (LTD) domain profile. / Intermediate filament protein, conserved site / Intermediate filament protein / Intermediate filament (IF) rod domain signature. / Intermediate filament, rod domain / Intermediate filament (IF) rod domain profile. / Intermediate filament protein / Linker histone H1/H5 / linker histone H1 and H5 family / Linker histone H1/H5, domain H15 / Linker histone H1/H5 globular (H15) domain profile. / Domain in histone families 1 and 5 / : / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Barrier-to-autointegration factor / Prelamin-A/C / Histone H2A type 1-B/E / Histone H2B type 1-J / Histone H4 / Histone H3.1 / Histone H1.1
Similarity search - Component
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.05 Å
AuthorsHorikoshi N / Miyake R / Sogawa-Fujiwara C / Ogasawara M / Takizawa Y / Kurumizaka H
Funding support Japan, 10 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP22K06076 Japan
Japan Society for the Promotion of Science (JSPS)JP23K24013 Japan
Japan Society for the Promotion of Science (JSPS)JP24H02328 Japan
Japan Society for the Promotion of Science (JSPS)JP22K06098 Japan
Japan Society for the Promotion of Science (JSPS)JP24H02319 Japan
Japan Society for the Promotion of Science (JSPS)JP24H02328 Japan
Japan Society for the Promotion of Science (JSPS)JP23H05475 Japan
Japan Science and TechnologyJPMJER1901 Japan
Japan Agency for Medical Research and Development (AMED)JP24ama121009 Japan
Japan Agency for Medical Research and Development (AMED)JP24ama121002 Japan
CitationJournal: Nat Commun / Year: 2025
Title: Cryo-EM structures of the BAF-Lamin A/C complex bound to nucleosomes.
Authors: Naoki Horikoshi / Ryosuke Miyake / Chizuru Sogawa-Fujiwara / Mitsuo Ogasawara / Yoshimasa Takizawa / Hitoshi Kurumizaka /
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 ...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.
History
DepositionAug 21, 2024-
Header (metadata) releaseFeb 26, 2025-
Map releaseFeb 26, 2025-
UpdateFeb 26, 2025-
Current statusFeb 26, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_61233.png

Downloads & links

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Map

FileDownload / File: emd_61233.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 256 pix.
= 271.36 Å		1.06 Å/pix.
x 256 pix.
= 271.36 Å		1.06 Å/pix.
x 256 pix.
= 271.36 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00667
Minimum - Maximum-0.009267328 - 0.032064628
Average (Standard dev.)0.0005220755 (±0.0020793471)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 271.36 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_61233_msk_1.map
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Additional map: #1

Fileemd_61233_additional_1.map
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Half map: #2

Fileemd_61233_half_map_1.map
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Half map: #1

Fileemd_61233_half_map_2.map
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Sample components

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Entire : Complex containing BAF, Lamin A/C IgF, H1, and nucleosome

EntireName: Complex containing BAF, Lamin A/C IgF, H1, and nucleosome
Components
  • Complex: Complex containing BAF, Lamin A/C IgF, H1, and nucleosome
    • Protein or peptide: Histone H3.1
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A type 1-B/E
    • Protein or peptide: Histone H2B type 1-J
    • DNA: DNA (193-MER)
    • DNA: DNA (193-MER)
    • Protein or peptide: Barrier-to-autointegration factor
    • Protein or peptide: Lamin-A/C
    • Protein or peptide: Histone H1.1

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Supramolecule #1: Complex containing BAF, Lamin A/C IgF, H1, and nucleosome

SupramoleculeName: Complex containing BAF, Lamin A/C IgF, H1, and nucleosome
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#9
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 580 KDa

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Macromolecule #1: Histone H3.1

MacromoleculeName: Histone H3.1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.719445 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSHMARTKQT ARKSTGGKAP RKQLATKAAR KSAPATGGVK KPHRYRPGTV ALREIRRYQK STELLIRKLP FQRLVREIAQ DFKTDLRFQ SSAVMALQEA CEAYLVGLFE DTNLCAIHAK RVTIMPKDIQ LARRIRGERA

UniProtKB: Histone H3.1

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Macromolecule #2: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.676703 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSHMSGRGKG GKGLGKGGAK RHRKVLRDNI QGITKPAIRR LARRGGVKRI SGLIYEETRG VLKVFLENVI RDAVTYTEHA KRKTVTAMD VVYALKRQGR TLYGFGG

UniProtKB: Histone H4

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Macromolecule #3: Histone H2A type 1-B/E

MacromoleculeName: Histone H2A type 1-B/E / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.447825 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSHMSGRGKQ GGKARAKAKT RSSRAGLQFP VGRVHRLLRK GNYSERVGAG APVYLAAVLE YLTAEILELA GNAARDNKKT RIIPRHLQL AIRNDEELNK LLGRVTIAQG GVLPNIQAVL LPKKTESHHK AKGK

UniProtKB: Histone H2A type 1-B/E

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Macromolecule #4: Histone H2B type 1-J

MacromoleculeName: Histone H2B type 1-J / type: protein_or_peptide / ID: 4 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.217516 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSHMPEPAKS APAPKKGSKK AVTKAQKKDG KKRKRSRKES YSIYVYKVLK QVHPDTGISS KAMGIMNSFV NDIFERIAGE ASRLAHYNK RSTITSREIQ TAVRLLLPGE LAKHAVSEGT KAVTKYTSAK

UniProtKB: Histone H2B type 1-J

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Macromolecule #7: Barrier-to-autointegration factor

MacromoleculeName: Barrier-to-autointegration factor / type: protein_or_peptide / ID: 7 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.487059 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSHMMTTSQK HRDFVAEPMG EKPVGSLAGI GEVLGKKLEE RGFDKAYVVL GQFLVLKKDE DLFREWLKDT CGANAKQSRD CFGCLREWC DAFL

UniProtKB: Barrier-to-autointegration factor

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Macromolecule #8: Lamin-A/C

MacromoleculeName: Lamin-A/C / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 17.551369 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SHGGGSVTKK RKLESTESRS SFSQHARTSG RVAVEEVDEE GKFVRLRNKS NEDQSMGNWQ IKRQNGDDPL LTYRFPPKFT LKAGQVVTI WAAGAGATHS PPTDLVWKAQ NTWGCGNSLR TALINSTGEE VAMRKLVRSV TVVEDDEDED GDDLLHHHH

UniProtKB: Prelamin-A/C

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Macromolecule #9: Histone H1.1

MacromoleculeName: Histone H1.1 / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.633172 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSETVPPAPA ASAAPEKPLA GKKAKKPAKA AAASKKKPAG PSVSELIVQA ASSSKERGGV SLAALKKALA AAGYDVEKNN SRIKLGIKS LVSKGTLVQT KGTGASGSFK LNKKASSVET KPGASKVATK TKATGASKKL KKATGASKKS VKTPKKAKKP A ATRKSSKN ...String:
MSETVPPAPA ASAAPEKPLA GKKAKKPAKA AAASKKKPAG PSVSELIVQA ASSSKERGGV SLAALKKALA AAGYDVEKNN SRIKLGIKS LVSKGTLVQT KGTGASGSFK LNKKASSVET KPGASKVATK TKATGASKKL KKATGASKKS VKTPKKAKKP A ATRKSSKN PKKPKTVKPK KVAKSPAKAK AVKPKAAKAR VTKPKTAKPK KAAPKKKLEV LFQ

UniProtKB: Histone H1.1

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Macromolecule #5: DNA (193-MER)

MacromoleculeName: DNA (193-MER) / type: dna / ID: 5 / Number of copies: 2 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 59.351793 KDa
SequenceString: (DA)(DT)(DC)(DG)(DG)(DA)(DC)(DC)(DC)(DT) (DA)(DT)(DC)(DG)(DC)(DG)(DA)(DG)(DC)(DC) (DA)(DG)(DG)(DC)(DC)(DT)(DG)(DA)(DG) (DA)(DA)(DT)(DC)(DC)(DG)(DG)(DT)(DG)(DC) (DC) (DG)(DA)(DG)(DG)(DC)(DC) ...String:
(DA)(DT)(DC)(DG)(DG)(DA)(DC)(DC)(DC)(DT) (DA)(DT)(DC)(DG)(DC)(DG)(DA)(DG)(DC)(DC) (DA)(DG)(DG)(DC)(DC)(DT)(DG)(DA)(DG) (DA)(DA)(DT)(DC)(DC)(DG)(DG)(DT)(DG)(DC) (DC) (DG)(DA)(DG)(DG)(DC)(DC)(DG)(DC) (DT)(DC)(DA)(DA)(DT)(DT)(DG)(DG)(DT)(DC) (DG)(DT) (DA)(DG)(DA)(DC)(DA)(DG)(DC) (DT)(DC)(DT)(DA)(DG)(DC)(DA)(DC)(DC)(DG) (DC)(DT)(DT) (DA)(DA)(DA)(DC)(DG)(DC) (DA)(DC)(DG)(DT)(DA)(DC)(DG)(DC)(DG)(DC) (DT)(DG)(DT)(DC) (DC)(DC)(DC)(DC)(DG) (DC)(DG)(DT)(DT)(DT)(DT)(DA)(DA)(DC)(DC) (DG)(DC)(DC)(DA)(DA) (DG)(DG)(DG)(DG) (DA)(DT)(DT)(DA)(DC)(DT)(DC)(DC)(DC)(DT) (DA)(DG)(DT)(DC)(DT)(DC) (DC)(DA)(DG) (DG)(DC)(DA)(DC)(DG)(DT)(DG)(DT)(DC)(DA) (DG)(DA)(DT)(DA)(DT)(DA)(DT) (DA)(DC) (DA)(DT)(DC)(DC)(DA)(DG)(DG)(DC)(DC)(DT) (DT)(DG)(DT)(DG)(DT)(DC)(DG)(DC) (DG) (DA)(DA)(DA)(DT)(DT)(DC)(DA)(DT)(DA)(DG) (DA)(DT)

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Macromolecule #6: DNA (193-MER)

MacromoleculeName: DNA (193-MER) / type: dna / ID: 6 / Number of copies: 2 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 59.823086 KDa
SequenceString: (DA)(DT)(DC)(DT)(DA)(DT)(DG)(DA)(DA)(DT) (DT)(DT)(DC)(DG)(DC)(DG)(DA)(DC)(DA)(DC) (DA)(DA)(DG)(DG)(DC)(DC)(DT)(DG)(DG) (DA)(DT)(DG)(DT)(DA)(DT)(DA)(DT)(DA)(DT) (DC) (DT)(DG)(DA)(DC)(DA)(DC) ...String:
(DA)(DT)(DC)(DT)(DA)(DT)(DG)(DA)(DA)(DT) (DT)(DT)(DC)(DG)(DC)(DG)(DA)(DC)(DA)(DC) (DA)(DA)(DG)(DG)(DC)(DC)(DT)(DG)(DG) (DA)(DT)(DG)(DT)(DA)(DT)(DA)(DT)(DA)(DT) (DC) (DT)(DG)(DA)(DC)(DA)(DC)(DG)(DT) (DG)(DC)(DC)(DT)(DG)(DG)(DA)(DG)(DA)(DC) (DT)(DA) (DG)(DG)(DG)(DA)(DG)(DT)(DA) (DA)(DT)(DC)(DC)(DC)(DC)(DT)(DT)(DG)(DG) (DC)(DG)(DG) (DT)(DT)(DA)(DA)(DA)(DA) (DC)(DG)(DC)(DG)(DG)(DG)(DG)(DG)(DA)(DC) (DA)(DG)(DC)(DG) (DC)(DG)(DT)(DA)(DC) (DG)(DT)(DG)(DC)(DG)(DT)(DT)(DT)(DA)(DA) (DG)(DC)(DG)(DG)(DT) (DG)(DC)(DT)(DA) (DG)(DA)(DG)(DC)(DT)(DG)(DT)(DC)(DT)(DA) (DC)(DG)(DA)(DC)(DC)(DA) (DA)(DT)(DT) (DG)(DA)(DG)(DC)(DG)(DG)(DC)(DC)(DT)(DC) (DG)(DG)(DC)(DA)(DC)(DC)(DG) (DG)(DA) (DT)(DT)(DC)(DT)(DC)(DA)(DG)(DG)(DC)(DC) (DT)(DG)(DG)(DC)(DT)(DC)(DG)(DC) (DG) (DA)(DT)(DA)(DG)(DG)(DG)(DT)(DC)(DC)(DG) (DA)(DT)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 59.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.05 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 152402
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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