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- EMDB-51375: BCL7A and BAF47 in a nucleosome bound state -

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Basic information

Entry
Database: EMDB / ID: EMD-51375
TitleBCL7A and BAF47 in a nucleosome bound state
Map data
Sample
  • Complex: nucleosome-bound human BCL7A
    • Protein or peptide: Histone H3.2
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2B
    • Protein or peptide: Histone H2A
    • Protein or peptide: BAF47
    • Protein or peptide: BCL7A
KeywordsNucleosome / acidic patch / BCL7A / arginine anchor / STRUCTURAL PROTEIN
Biological speciesHomo sapiens (human) / Xenopus laevis (African clawed frog)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.34 Å
AuthorsMartin F / Bergamin E
Funding support France, 3 items
OrganizationGrant numberCountry
ATIP-Avenir France
Fondation pour la Recherche Medicale (FRM) France
Fondation ARC France
CitationJournal: Nucleic Acids Res / Year: 2025
Title: Structure of the nucleosome-bound human BCL7A.
Authors: Franck Martin / Asgar Abbas Kazrani / Julie Lafouge / Dana Mariel Diaz-Jimenez / Stéphanie Siebert / Leonie Fabbro-Burtschell / Emma Maillard / Karine Lapouge / Haydyn David Thomas Mertens ...Authors: Franck Martin / Asgar Abbas Kazrani / Julie Lafouge / Dana Mariel Diaz-Jimenez / Stéphanie Siebert / Leonie Fabbro-Burtschell / Emma Maillard / Karine Lapouge / Haydyn David Thomas Mertens / Claude Sauter / Alexander Leitner / Françoise Ochsenbein / Alexandre Blais / Elisa Bergamin /
Abstract: Proteins of the BCL7 family (BCL7A, BCL7B, and BCL7C) are among the most recently identified subunits of the mammalian SWI/SNF chromatin remodeler complex and are absent from the unicellular version ...Proteins of the BCL7 family (BCL7A, BCL7B, and BCL7C) are among the most recently identified subunits of the mammalian SWI/SNF chromatin remodeler complex and are absent from the unicellular version of this complex. Their function in the complex is unknown, and very limited structural information is available, despite the fact that they are mutated in several cancer types, most notably blood malignancies and hence medically relevant. Here, using cryo-electron microscopy in combination with biophysical and biochemical approaches, we show that BCL7A forms a stable, high-affinity complex with the nucleosome core particle (NCP) through binding of BCL7A with the acidic patch of the nucleosome via an arginine anchor motif. This interaction is impaired by BCL7A mutations found in cancer. Further, we determined that BCL7A contributes to the remodeling activity of the mSWI/SNF complex and we examined its function at the genomic level. Our findings reveal how BCL7 proteins interact with the NCP and help rationalize the impact of cancer-associated mutations. By providing structural information on the positioning of BCL7 on the NCP, our results broaden the understanding of the mechanism by which SWI/SNF recognizes the chromatin fiber.
History
DepositionAug 19, 2024-
Header (metadata) releaseApr 23, 2025-
Map releaseApr 23, 2025-
UpdateApr 23, 2025-
Current statusApr 23, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51375.png

Downloads & links

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Map

FileDownload / File: emd_51375.map.gz / Format: CCP4 / Size: 137.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.9 Å/pix.
x 330 pix.
= 297.33 Å		0.9 Å/pix.
x 330 pix.
= 297.33 Å		0.9 Å/pix.
x 330 pix.
= 297.33 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.901 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.10229811 - 0.36414883
Average (Standard dev.)0.0002406688 (±0.013758673)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions330330330
Spacing330330330
CellA=B=C: 297.33002 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_51375_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_51375_half_map_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_51375_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : nucleosome-bound human BCL7A

EntireName: nucleosome-bound human BCL7A
Components
  • Complex: nucleosome-bound human BCL7A
    • Protein or peptide: Histone H3.2
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2B
    • Protein or peptide: Histone H2A
    • Protein or peptide: BAF47
    • Protein or peptide: BCL7A

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Supramolecule #1: nucleosome-bound human BCL7A

SupramoleculeName: nucleosome-bound human BCL7A / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2, #4, #3, #5-#6
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Histone H3.2

MacromoleculeName: Histone H3.2 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
ARTKQTARKS TGGKAPRKQL ATKAARKSAP ATGGVKKPHR YRPGTVALRE IRRYQKSTEL LIRKLPFQRL VREIAQDFKT DLRFQSSAVM ALQEASEAYL VALFEDTNLC AIHAKRVTIM PKDIQLARRI RGERA

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Macromolecule #2: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SGRGKGGKGL GKGGAKRHRK VLRDNIQGIT KPAIRRLARR GGVKRISGLI YEETRGVLKV FLENVIRDAV TYTEHAKRKT VTAMDVVYAL KRQGRTLYGF GG

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Macromolecule #3: Histone H2A

MacromoleculeName: Histone H2A / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SGRGKQGGKT RAKAKTRSSR AGLQFPVGRV HRLLRKGNYA ERVGAGAPVY LAAVLEYLTA EILELAGNAA RDNKKTRIIP RHLQLAVRND EELNKLLGRV TIAQGGVLPN IQSVLLPKK

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Macromolecule #4: Histone H2B

MacromoleculeName: Histone H2B / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
PEPAKSAPAP KKGSKKAVTK TQKKDGKKRR KTRKESYAIY VYKVLKQVHP DTGISSKAMS IMNSFVNDVF ERIAGEASRL AHYNKRSTIT SREIQTAVRL LLPGELAKHA VSEGTKAVTK YTSAK

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Macromolecule #5: BAF47

MacromoleculeName: BAF47 / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MMMMALSKTF GQKPVKFQLE DDGEFYMIGS EVGNYLRMFR GSLYKRYPSL WRRLATVEER KKIVASSHG KKTKPNTKDH GYTTLATSVT LLKASEVEEI LDGNDEKYKA VSISTEPPTY L REQKAKRN SQWVPTLPNS SHHLDAVPCS TTINRNRMGR DKKRTFPLCF ...String:
MMMMALSKTF GQKPVKFQLE DDGEFYMIGS EVGNYLRMFR GSLYKRYPSL WRRLATVEER KKIVASSHG KKTKPNTKDH GYTTLATSVT LLKASEVEEI LDGNDEKYKA VSISTEPPTY L REQKAKRN SQWVPTLPNS SHHLDAVPCS TTINRNRMGR DKKRTFPLCF DDHDPAVIHE NA SQPEVLV PIRLDMEIDG QKLRDAFTWN MNEKLMTPEM FSEILCDDLD LNPLTFVPAI ASA IRQQIE SYPTDSILED QSDQRVIIKL NIHVGNISLV DQFEWDMSEK ENSPEKFALK LCSE LGLGG EFVTTIAYSI RGQLSWHQKT YAFSENPLPT VEIAIRNTGD ADQWCPLLET LTDAE MEKK IRDQDRNTRR MRRLANTAPA W

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Macromolecule #6: BCL7A

MacromoleculeName: BCL7A / type: protein_or_peptide / ID: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSGRSVRAET RSRAKDDIKR VMAAIEKVRK WEKKWVTVGD TSLRIYKWVP VTEPKVDDKN KNKKKGKDE KCGSEVTTPE NSSSPGMMDM HDDNSNQSSI ADASPIKQEN SSNSSPAPEP N SAVPSDGT EAKVDEAQAD GKEHPGAEDA SDEQNSQSSM EHSMNSSEKV ...String:
MSGRSVRAET RSRAKDDIKR VMAAIEKVRK WEKKWVTVGD TSLRIYKWVP VTEPKVDDKN KNKKKGKDE KCGSEVTTPE NSSSPGMMDM HDDNSNQSSI ADASPIKQEN SSNSSPAPEP N SAVPSDGT EAKVDEAQAD GKEHPGAEDA SDEQNSQSSM EHSMNSSEKV DRQPSGDSGL AA ETSAISQ VPRSRSQRGS QIGREPIGLS GDLEGVPPSK KMKLEASQQN SEEM

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.93 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3lz1

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.34 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 510009
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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