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- EMDB-0974: Structure of nucleosome-bound human BAF complex -

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Basic information

Entry
Database: EMDB / ID: EMD-0974
TitleStructure of nucleosome-bound human BAF complex
Map data
SampleStructure of nucleosome-bound human BAF complex
  • Nucleosome
  • BAF
  • Histone H3.3H3F3A
  • Histone H4
  • Histone H2A type 1
  • Histone H2B
  • Transcription activator BRG1
  • Actin-like protein 6A
  • Actin, cytoplasmic 1
  • AT-rich interactive domain-containing protein 1A
  • (SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily ...) x 3
  • SWI/SNF complex subunit SMARCC2
  • Zinc finger protein ubi-d4
  • (nucleic-acidNucleic acid) x 2
  • ligand
Function / homology
Function and homology information


optic cup formation involved in camera-type eye development / cardiac chamber development / formation of primary germ layer / negative regulation of myeloid progenitor cell differentiation / H3K9me3 modified histone binding / single stranded viral RNA replication via double stranded DNA intermediate / negative regulation of histone H3-K9 dimethylation / positive regulation of norepinephrine uptake / cellular response to cytochalasin B / brahma complex ...optic cup formation involved in camera-type eye development / cardiac chamber development / formation of primary germ layer / negative regulation of myeloid progenitor cell differentiation / H3K9me3 modified histone binding / single stranded viral RNA replication via double stranded DNA intermediate / negative regulation of histone H3-K9 dimethylation / positive regulation of norepinephrine uptake / cellular response to cytochalasin B / brahma complex / positive regulation of glucose mediated signaling pathway / npBAF complex / regulation of transepithelial transport / positive regulation of histone H4 acetylation / nBAF complex / heterochromatin maintenance / morphogenesis of a polarized epithelium / glucocorticoid receptor signaling pathway / histone H2A acetylation / protein localization to adherens junction / structural constituent of postsynaptic actin cytoskeleton / postsynaptic actin cytoskeleton organization / Tat protein binding / negative regulation of androgen receptor signaling pathway / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / dense body / neural retina development / regulation of norepinephrine uptake / blastocyst formation / RNA polymerase I core promoter sequence-specific DNA binding / positive regulation of histone H3-K9 acetylation / apical protein localization / cardiac muscle cell differentiation / Ino80 complex / nucleosome mobilization / placenta blood vessel development / nucleosome disassembly / adherens junction assembly / tight junction / SWI/SNF complex / positive regulation by host of viral transcription / nucleosome binding / androgen receptor signaling pathway / NuA4 histone acetyltransferase complex / positive regulation of gene expression, epigenetic / apical junction complex / neurogenesis / chromatin-mediated maintenance of transcription / cell junction assembly / maintenance of blood-brain barrier / toxin transport / kinesin binding / regulation of growth / ATP-dependent chromatin remodeling / stem cell population maintenance / cellular response to fatty acid / androgen receptor binding / negative regulation of histone H3-K9 trimethylation / spinal cord development / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / beta-catenin-TCF complex assembly / establishment or maintenance of cell polarity / N-acetyltransferase activity / histone H4 acetylation / positive regulation of Wnt signaling pathway / regulation of cyclin-dependent protein serine/threonine kinase activity / DNA-dependent ATPase activity / interleukin-7-mediated signaling pathway / nitric-oxide synthase binding / DNA polymerase binding / molecular adaptor activity / regulation of protein localization to plasma membrane / intracellular estrogen receptor signaling pathway / cell motility / substantia nigra development / forebrain development / axonogenesis / presynapse / regulation of transmembrane transporter activity / embryo implantation / nuclear receptor binding / actin filament / nuclear chromosome / DNA-templated transcription, initiation / neural tube closure / apoptotic signaling pathway / positive regulation of pri-miRNA transcription by RNA polymerase II / fibrillar center / lysine-acetylated histone binding / adherens junction / structural constituent of cytoskeleton / cytoplasmic ribonucleoprotein granule / tau protein binding / nucleosome / ephrin receptor signaling pathway / platelet aggregation / transcription coregulator activity / negative regulation of protein binding / transcription corepressor activity / nervous system development
Actin, conserved site / Helicase superfamily 1/2, ATP-binding domain / High mobility group box domain / Histone-fold / Zinc finger, FYVE/PHD-type / Armadillo-like helical / Zinc finger, RING/FYVE/PHD-type / Zinc finger C2H2-type / Helicase/SANT-associated domain / SWIRM domain ...Actin, conserved site / Helicase superfamily 1/2, ATP-binding domain / High mobility group box domain / Histone-fold / Zinc finger, FYVE/PHD-type / Armadillo-like helical / Zinc finger, RING/FYVE/PHD-type / Zinc finger C2H2-type / Helicase/SANT-associated domain / SWIRM domain / Glutamine-Leucine-Glutamine, QLQ / Armadillo-type fold / Chromatin-remodeling complex component Sfh1/SNF5 / SANT domain / Bromodomain, conserved site / Zinc finger, PHD-finger / Homeobox-like domain superfamily / Histone H2A/H2B/H3 / SWIB domain / ARID DNA-binding domain / Histone H3/CENP-A / SNF2-related domain / Histone H2B / Chromo/chromo shadow domain / SANT/Myb domain / Bromodomain / Helicase, C-terminal / BRK domain / Histone H4 / Zinc finger, PHD-type / Histone H2A / SWIB/MDM2 domain / Actin family / TATA box binding protein associated factor (TAF) / Histone H4, conserved site / SNF5/SMARCB1/INI1 / Actin/actin-like conserved site / CENP-T/Histone H4, histone fold / SNF2-like, N-terminal domain superfamily / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1 / BRK domain superfamily / ATPase, nucleotide binding domain / SWI/SNF-like complex subunit BAF250/Osa / High mobility group box domain superfamily / SWIB/MDM2 domain superfamily / ARID DNA-binding domain superfamily / Bromodomain-like superfamily / BRCT domain superfamily / Winged helix-like DNA-binding domain superfamily / Zinc finger C2H2 superfamily / SWI/SNF complex subunit SMARCC2 / SWI/SNF-like complex subunit BAF250, C-terminal / Snf2, ATP coupling domain / SMARCC, SWIRM-associated domain / Histone H2A conserved site / SWI/SNF-like complex subunit BAF250a / SWI/SNF complex subunit BAF57 / SWI/SNF complex subunit BRG1 / SMARCC, N-terminal / SMARCC, C-terminal / Histone H2A, C-terminal domain / P-loop containing nucleoside triphosphate hydrolase / Requiem/DPF N-terminal domain
SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1 / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1 / Zinc finger protein ubi-d4 / Histone H2B / SWI/SNF complex subunit SMARCC2 / Histone H3.3 / AT-rich interactive domain-containing protein 1A / Histone H4 / Actin, cytoplasmic 1 / Transcription activator BRG1 ...SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1 / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1 / Zinc finger protein ubi-d4 / Histone H2B / SWI/SNF complex subunit SMARCC2 / Histone H3.3 / AT-rich interactive domain-containing protein 1A / Histone H4 / Actin, cytoplasmic 1 / Transcription activator BRG1 / Histone H2A type 1 / Histone H2B 1.1 / Actin-like protein 6A / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1
Biological speciesXenopus calcaratus (Biafran clawed frog) / Homo sapiens (human) / Xenopus laevis (African clawed frog)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsShuang H / Zihan W / Yuan T / Zishuo Y / Jiali Y / Xinxin W / Jie L / Bijun L / Yanhui X
CitationJournal: Science / Year: 2020
Title: Structure of nucleosome-bound human BAF complex.
Authors: Shuang He / Zihan Wu / Yuan Tian / Zishuo Yu / Jiali Yu / Xinxin Wang / Jie Li / Bijun Liu / Yanhui Xu /
Abstract: Mammalian SWI/SNF family chromatin remodelers, BRG1/BRM-associated factor (BAF) and polybromo-associated BAF (PBAF), regulate chromatin structure and transcription, and their mutations are linked to ...Mammalian SWI/SNF family chromatin remodelers, BRG1/BRM-associated factor (BAF) and polybromo-associated BAF (PBAF), regulate chromatin structure and transcription, and their mutations are linked to cancers. The 3.7-angstrom-resolution cryo-electron microscopy structure of human BAF bound to the nucleosome reveals that the nucleosome is sandwiched by the base and the adenosine triphosphatase (ATPase) modules, which are bridged by the actin-related protein (ARP) module. The ATPase motor is positioned proximal to nucleosomal DNA and, upon ATP hydrolysis, engages with and pumps DNA along the nucleosome. The C-terminal α helix of SMARCB1, enriched in positively charged residues frequently mutated in cancers, mediates interactions with an acidic patch of the nucleosome. AT-rich interactive domain-containing protein 1A (ARID1A) and the SWI/SNF complex subunit SMARCC serve as a structural core and scaffold in the base module organization, respectively. Our study provides structural insights into subunit organization and nucleosome recognition of human BAF complex.
Validation ReportSummary, Full report, XML, About validation report
History
DepositionJan 22, 2020-
Header (metadata) releaseFeb 12, 2020-
Map releaseFeb 12, 2020-
UpdateFeb 12, 2020-
Current statusFeb 12, 2020Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.6
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.6
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0974.png

Downloads & links

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Map

FileDownload / File: emd_0974.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 512 pix.
= 532.48 Å		1.04 Å/pix.
x 512 pix.
= 532.48 Å		1.04 Å/pix.
x 512 pix.
= 532.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.48 / Movie #1: 0.6
Minimum - Maximum-1.2884388 - 3.305587
Average (Standard dev.)-0.0000662169 (±0.107257016)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 532.48 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.041.041.04
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z532.480532.480532.480
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS512512512
D min/max/mean-1.2883.306-0.000

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Supplemental data

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Sample components

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Entire Structure of nucleosome-bound human BAF complex

EntireName: Structure of nucleosome-bound human BAF complex / Number of components: 19

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Component #1: protein, Structure of nucleosome-bound human BAF complex

ProteinName: Structure of nucleosome-bound human BAF complex / Recombinant expression: No

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Component #2: protein, Nucleosome

ProteinName: Nucleosome / Recombinant expression: No
SourceSpecies: Xenopus calcaratus (Biafran clawed frog)
Source (engineered)Expression System: Escherichia coli BL21 (bacteria) / Strain: BL21

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Component #3: protein, BAF

ProteinName: BAF / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human) / Cell of expression system: HEK293T

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Component #4: protein, Histone H3.3

ProteinName: Histone H3.3H3F3A / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 15.360983 kDa
SourceSpecies: Xenopus laevis (African clawed frog)
Source (engineered)Expression System: Escherichia coli BL21 (bacteria)

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Component #5: protein, Histone H4

ProteinName: Histone H4 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 11.394426 kDa
SourceSpecies: Xenopus laevis (African clawed frog)
Source (engineered)Expression System: Escherichia coli BL21 (bacteria)

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Component #6: protein, Histone H2A type 1

ProteinName: Histone H2A type 1 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 13.993295 kDa
SourceSpecies: Xenopus laevis (African clawed frog)
Source (engineered)Expression System: Escherichia coli BL21 (bacteria)

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Component #7: protein, Histone H2B

ProteinName: Histone H2B / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 13.873086 kDa
SourceSpecies: Xenopus laevis (African clawed frog)
Source (engineered)Expression System: Escherichia coli BL21 (bacteria)

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Component #8: protein, Transcription activator BRG1

ProteinName: Transcription activator BRG1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 184.923828 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #9: protein, Actin-like protein 6A

ProteinName: Actin-like protein 6A / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 45.236273 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #10: protein, Actin, cytoplasmic 1

ProteinName: Actin, cytoplasmic 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 41.78266 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #11: protein, AT-rich interactive domain-containing protein 1A

ProteinName: AT-rich interactive domain-containing protein 1A / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 142.316531 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #12: protein, SWI/SNF-related matrix-associated actin-dependent regula...

ProteinName: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 38.015094 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #13: protein, SWI/SNF complex subunit SMARCC2

ProteinName: SWI/SNF complex subunit SMARCC2 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 133.048109 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #14: protein, SWI/SNF-related matrix-associated actin-dependent regula...

ProteinName: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 58.311391 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #15: protein, SWI/SNF-related matrix-associated actin-dependent regula...

ProteinName: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 46.710371 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #16: protein, Zinc finger protein ubi-d4

ProteinName: Zinc finger protein ubi-d4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 32.781926 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #17: nucleic-acid, DNA (119-MER)

nucleic acidName: DNA (119-MER) / Class: DNA / Structure: OTHER / Synthetic: No
Sequence: (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) ...Sequence:
(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)
MassTheoretical: 36.520266 kDa
SourceSpecies: Homo sapiens (human)

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Component #18: nucleic-acid, DNA (119-MER)

nucleic acidName: DNA (119-MER) / Class: DNA / Structure: OTHER / Synthetic: No
Sequence: (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) ...Sequence:
(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)
MassTheoretical: 36.92952 kDa
SourceSpecies: Homo sapiens (human)

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Component #19: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 8
VitrificationCryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 50 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: OTHER
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 320658
3D reconstructionSoftware: RELION / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

6ltj

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