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- EMDB-65853: The structure of NCP-RA module of ncBAF-nucleosome complex -

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Basic information

Entry
Database: EMDB / ID: EMD-65853
TitleThe structure of NCP-RA module of ncBAF-nucleosome complex
Map dataThe structure of BCL7A bound to the nucleosome
Sample
  • Complex: NCP-RA of ncBAF
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A
    • Protein or peptide: Histone H2B 1.1
    • Protein or peptide: Histone H3.2
    • DNA: DNA (207-MER)
    • DNA: DNA (207-MER)
    • Protein or peptide: B-cell CLL/lymphoma 7 protein family member A
KeywordsChromatin remodeling complex / GENE REGULATION/DNA / GENE REGULATION-DNA complex
Function / homology
Function and homology information


Formation of the polybromo-BAF (pBAF) complex / Formation of the non-canonical BAF (ncBAF) complex / Formation of the canonical BAF (cBAF) complex / Formation of the embryonic stem cell BAF (esBAF) complex / Formation of neuronal progenitor and neuronal BAF (npBAF and nBAF) / neuron projection arborization / GBAF complex / regulation of G0 to G1 transition / regulation of nucleotide-excision repair / SWI/SNF complex ...Formation of the polybromo-BAF (pBAF) complex / Formation of the non-canonical BAF (ncBAF) complex / Formation of the canonical BAF (cBAF) complex / Formation of the embryonic stem cell BAF (esBAF) complex / Formation of neuronal progenitor and neuronal BAF (npBAF and nBAF) / neuron projection arborization / GBAF complex / regulation of G0 to G1 transition / regulation of nucleotide-excision repair / SWI/SNF complex / regulation of mitotic metaphase/anaphase transition / positive regulation of double-strand break repair / positive regulation of stem cell population maintenance / motor behavior / Regulation of MITF-M-dependent genes involved in pigmentation / regulation of G1/S transition of mitotic cell cycle / negative regulation of cell differentiation / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / structural constituent of chromatin / heterochromatin formation / nucleosome / nucleosome assembly / chromatin remodeling / protein heterodimerization activity / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / regulation of transcription by RNA polymerase II / chromatin / DNA binding / nucleoplasm / nucleus
Similarity search - Function
BCL7 / BCL7, N-terminal conserver region / : / Histone H2A conserved site / Histone H2A signature. / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A ...BCL7 / BCL7, N-terminal conserver region / : / Histone H2A conserved site / Histone H2A signature. / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / 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 domain / Histone-fold
Similarity search - Domain/homology
Histone H2B 1.1 / Histone H4 / Histone H3.2 / B-cell CLL/lymphoma 7 protein family member A / Histone H2A
Similarity search - Component
Biological speciesHomo sapiens (human) / Xenopus laevis (African clawed frog) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsChen KJ / Chen ZC
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32130016 China
CitationJournal: Cell Discov / Year: 2025
Title: ncBAF recognizes the nucleosome through BCL7A in chromatin remodeling.
Authors: Kangjing Chen / Liwen Du / Yumin Liu / Mo Chen / Zhucheng Chen /
History
DepositionAug 15, 2025-
Header (metadata) releaseFeb 18, 2026-
Map releaseFeb 18, 2026-
UpdateFeb 18, 2026-
Current statusFeb 18, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65853.png

Downloads & links

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Map

FileDownload / File: emd_65853.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe structure of BCL7A bound to the nucleosome
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.54 Å/pix.
x 400 pix.
= 216.5 Å		0.54 Å/pix.
x 400 pix.
= 216.5 Å		0.54 Å/pix.
x 400 pix.
= 216.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.54125 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.017
Minimum - Maximum-0.043693215 - 0.16034715
Average (Standard dev.)0.00019307583 (±0.00532)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 216.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_65853_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_65853_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : NCP-RA of ncBAF

EntireName: NCP-RA of ncBAF
Components
  • Complex: NCP-RA of ncBAF
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A
    • Protein or peptide: Histone H2B 1.1
    • Protein or peptide: Histone H3.2
    • DNA: DNA (207-MER)
    • DNA: DNA (207-MER)
    • Protein or peptide: B-cell CLL/lymphoma 7 protein family member A

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Supramolecule #1: NCP-RA of ncBAF

SupramoleculeName: NCP-RA of ncBAF / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 11.263231 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SGRGKGGKGL GKGGAKRHRK VLRDNIQGIT KPAIRRLARR GGVKRISGLI YEETRGVLKV FLENVIRDAV TYTEHAKRKT VTAMDVVYA LKRQGRTLYG FGG

UniProtKB: Histone H4

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Macromolecule #2: Histone H2A

MacromoleculeName: Histone H2A / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 13.978241 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SGRGKQGGKT RAKAKTRSSR AGLQFPVGRV HRLLRKGNYA ERVGAGAPVY LAAVLEYLTA EILELAGNAA RDNKKTRIIP RHLQLAVRN DEELNKLLGR VTIAQGGVLP NIQSVLLPKK TESSKSAKSK

UniProtKB: Histone H2A

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Macromolecule #3: Histone H2B 1.1

MacromoleculeName: Histone H2B 1.1 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 13.83407 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
PEPAKSAPAP KKGSKKAVTK TQKKDGKKRR KSRKESYAIY VYKVLKQVHP DTGISSKAMS IMNSFVNDVF ERIAGEASRL AHYNKRSTI TSREIQTAVR LLLPGELAKH AVSEGTKAVT KYTSAK

UniProtKB: Histone H2B 1.1

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Macromolecule #4: Histone H3.2

MacromoleculeName: Histone H3.2 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 15.30393 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
ARTKQTARKS TGGKAPRKQL ATKAARKSAP ATGGVKKPHR YRPGTVALRE IRRYQKSTEL LIRKLPFQRL VREIAQDFKT DLRFQSSAV MALQEASEAY LVALFEDTNL CAIHAKRVTI MPKDIQLARR IRGERA

UniProtKB: Histone H3.2

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Macromolecule #7: B-cell CLL/lymphoma 7 protein family member A

MacromoleculeName: B-cell CLL/lymphoma 7 protein family member A / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.842938 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSGRSVRAET RSRAKDDIKR VMAAIEKVRK WEKKWVTVGD TSLRIYKWVP VTEPKVDDKN KNKKKGKDEK CGSEVTTPEN SSSPGMMDM HDDNSNQSSI ADASPIKQEN SSNSSPAPEP NSAVPSDGTE AKVDEAQADG KEHPGAEDAS DEQNSQSSME H SMNSSEKV ...String:
MSGRSVRAET RSRAKDDIKR VMAAIEKVRK WEKKWVTVGD TSLRIYKWVP VTEPKVDDKN KNKKKGKDEK CGSEVTTPEN SSSPGMMDM HDDNSNQSSI ADASPIKQEN SSNSSPAPEP NSAVPSDGTE AKVDEAQADG KEHPGAEDAS DEQNSQSSME H SMNSSEKV DRQPSGDSGL AAETSAISQD LEGVPPSKKM KLEASQQNSE EM

UniProtKB: B-cell CLL/lymphoma 7 protein family member A

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Macromolecule #5: DNA (207-MER)

MacromoleculeName: DNA (207-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 63.553496 KDa
SequenceString: (DG)(DG)(DA)(DC)(DC)(DC)(DT)(DA)(DT)(DA) (DC)(DG)(DC)(DG)(DG)(DC)(DC)(DG)(DC)(DC) (DC)(DT)(DG)(DG)(DA)(DG)(DA)(DA)(DT) (DC)(DC)(DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG) (DA) (DG)(DG)(DC)(DC)(DG)(DC) ...String:
(DG)(DG)(DA)(DC)(DC)(DC)(DT)(DA)(DT)(DA) (DC)(DG)(DC)(DG)(DG)(DC)(DC)(DG)(DC)(DC) (DC)(DT)(DG)(DG)(DA)(DG)(DA)(DA)(DT) (DC)(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)(DT)(DG)(DA)(DA)(DT)(DC)(DA)(DC) (DC)(DC)(DC)(DA)(DC)(DG)(DA)(DA) (DG) (DT)(DA)(DC)(DT)(DA)(DG)(DA)(DG)(DG)(DA) (DT)(DC)(DA)(DT)(DA)(DA)(DT)(DC)(DA) (DG)(DC)(DC)(DA)(DT)(DA)(DC)

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Macromolecule #6: DNA (207-MER)

MacromoleculeName: DNA (207-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 64.272871 KDa
SequenceString: (DG)(DT)(DA)(DT)(DG)(DG)(DC)(DT)(DG)(DA) (DT)(DT)(DA)(DT)(DG)(DA)(DT)(DC)(DC)(DT) (DC)(DT)(DA)(DG)(DT)(DA)(DC)(DT)(DT) (DC)(DG)(DT)(DG)(DG)(DG)(DG)(DT)(DG)(DA) (DT) (DT)(DC)(DA)(DG)(DG)(DA) ...String:
(DG)(DT)(DA)(DT)(DG)(DG)(DC)(DT)(DG)(DA) (DT)(DT)(DA)(DT)(DG)(DA)(DT)(DC)(DC)(DT) (DC)(DT)(DA)(DG)(DT)(DA)(DC)(DT)(DT) (DC)(DG)(DT)(DG)(DG)(DG)(DG)(DT)(DG)(DA) (DT) (DT)(DC)(DA)(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)(DG)(DA)(DT) (DT) (DC)(DT)(DC)(DC)(DA)(DG)(DG)(DG)(DC)(DG) (DG)(DC)(DC)(DG)(DC)(DG)(DT)(DA)(DT) (DA)(DG)(DG)(DG)(DT)(DC)(DC)

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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: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.4000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 635115
Initial angle assignmentType: OTHER
Final angle assignmentType: MAXIMUM LIKELIHOOD

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