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- PDB-6ltj: Structure of nucleosome-bound human BAF complex -

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Entry
Database: PDB / ID: 6ltj
TitleStructure of nucleosome-bound human BAF complex
Components
  • (DNA (119-MER)) x 2
  • (SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily ...) x 3
  • AT-rich interactive domain-containing protein 1A
  • Actin, cytoplasmic 1
  • Actin-like protein 6A
  • Histone H2A type 1
  • Histone H2B
  • Histone H3.3H3F3A
  • Histone H4
  • SWI/SNF complex subunit SMARCC2
  • Transcription activator BRG1
  • Zinc finger protein ubi-d4
KeywordsGENE REGULATION / Chromatin remodeler / Complex
Function / homology
Function and homology information


optic cup formation involved in camera-type eye development / cardiac chamber development / negative regulation of myeloid progenitor cell differentiation / H3K9me3 modified histone binding / formation of primary germ layer / single stranded viral RNA replication via double stranded DNA intermediate / negative regulation of histone H3-K9 dimethylation / positive regulation of norepinephrine uptake / maintenance of chromatin silencing / brahma complex ...optic cup formation involved in camera-type eye development / cardiac chamber development / negative regulation of myeloid progenitor cell differentiation / H3K9me3 modified histone binding / formation of primary germ layer / single stranded viral RNA replication via double stranded DNA intermediate / negative regulation of histone H3-K9 dimethylation / positive regulation of norepinephrine uptake / maintenance of chromatin silencing / brahma complex / positive regulation of glucose mediated signaling pathway / npBAF complex / cellular response to cytochalasin B / positive regulation of histone H4 acetylation / regulation of transepithelial transport / nBAF complex / protein localization to adherens junction / morphogenesis of a polarized epithelium / histone H2A acetylation / glucocorticoid receptor signaling pathway / structural constituent of postsynaptic actin cytoskeleton / neural retina development / postsynaptic actin cytoskeleton / blastocyst formation / negative regulation of androgen receptor signaling pathway / dense body / Tat protein binding / nucleosome mobilization / postsynaptic actin cytoskeleton organization / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / RNA polymerase I core promoter sequence-specific DNA binding / regulation of norepinephrine uptake / positive regulation of histone H3-K9 acetylation / apical protein localization / cardiac muscle cell differentiation / placenta blood vessel development / Ino80 complex / nucleosome disassembly / adherens junction assembly / SWI/SNF complex / tight junction / positive regulation by host of viral transcription / NuA4 histone acetyltransferase complex / nucleosome binding / positive regulation of gene expression, epigenetic / apical junction complex / neurogenesis / cell junction assembly / chromatin-mediated maintenance of transcription / toxin transport / ATP-dependent chromatin remodeling / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / kinesin binding / establishment or maintenance of cell polarity / stem cell population maintenance / regulation of growth / cellular response to fatty acid / nitric-oxide synthase binding / spinal cord development / cortical cytoskeleton / beta-catenin-TCF complex assembly / negative regulation of histone H3-K9 trimethylation / N-acetyltransferase activity / synaptic vesicle endocytosis / histone H4 acetylation / positive regulation of Wnt signaling pathway / regulation of cyclin-dependent protein serine/threonine kinase activity / molecular adaptor activity / interleukin-7-mediated signaling pathway / DNA-dependent ATPase activity / histone acetyltransferase complex / intracellular estrogen receptor signaling pathway / calyx of Held / DNA polymerase binding / positive regulation of pri-miRNA transcription by RNA polymerase II / adherens junction / cell motility / regulation of protein localization to plasma membrane / substantia nigra development / helicase activity / histone acetyltransferase activity / regulation of transmembrane transporter activity / forebrain development / embryo implantation / androgen receptor signaling pathway / axonogenesis / nuclear chromosome / androgen receptor binding / DNA-templated transcription, initiation / actin filament / presynapse / nuclear receptor binding / lysine-acetylated histone binding / structural constituent of cytoskeleton / apoptotic signaling pathway / platelet aggregation / fibrillar center / cytoplasmic ribonucleoprotein granule / Schaffer collateral - CA1 synapse / neural tube closure
N-terminal domain of DPF2/REQ. / SANT domain / Armadillo-like helical / Zinc finger, RING/FYVE/PHD-type / Zinc finger C2H2-type / Helicase superfamily 1/2, ATP-binding domain / Helicase/SANT-associated domain / Glutamine-Leucine-Glutamine, QLQ / Armadillo-type fold / Chromatin-remodeling complex component Sfh1/SNF5 ...N-terminal domain of DPF2/REQ. / SANT domain / Armadillo-like helical / Zinc finger, RING/FYVE/PHD-type / Zinc finger C2H2-type / Helicase superfamily 1/2, ATP-binding domain / Helicase/SANT-associated domain / Glutamine-Leucine-Glutamine, QLQ / Armadillo-type fold / Chromatin-remodeling complex component Sfh1/SNF5 / Bromodomain, conserved site / Histone-fold / Zinc finger, PHD-finger / Histone H4, conserved site / SWIB domain / Actin/actin-like conserved site / SWI/SNF-like complex subunit BAF250/Osa / Requiem/DPF N-terminal domain / P-loop containing nucleoside triphosphate hydrolase / Snf2, ATP coupling domain / Zinc finger, FYVE/PHD-type / High mobility group box domain / SWI/SNF-like complex subunit BAF250a / Zinc finger, PHD-type / SNF2-related, N-terminal domain / Histone H2B / Chromo/chromo shadow domain / SANT/Myb domain / Bromodomain / ARID DNA-binding domain / Helicase, C-terminal / Histone H4 / Histone H2A / Homeobox-like domain superfamily / SWIB/MDM2 domain / Actin family / Actin, conserved site / TATA box binding protein associated factor (TAF) / BRK domain / SNF5/SMARCB1/INI1 / Histone H2A/H2B/H3 / SWIRM domain / SWI/SNF complex subunit BAF57 / SWI/SNF complex subunit BRG1 / Histone H3/CENP-A / SWI/SNF-like complex subunit BAF250/Osa / Bromodomain / HSA / BRK domain / QLQ / Snf2-ATP coupling, chromatin remodelling complex / Actin / ARID/BRIGHT DNA binding domain / SNF5 / SMARCB1 / INI1 / SMARCC, SWIRM-associated domain / Myb-like DNA-binding domain / SWIRM domain / SWIRM-associated region 1 / SWIRM-associated domain at the N-terminal / SWIRM-associated domain at the C-terminal / SWIB/MDM2 domain / HMG (high mobility group) box / PHD-finger / Helicase conserved C-terminal domain / SNF2 family N-terminal domain / C-terminus of histone H2A / Bromodomain-like superfamily / SMARCC, N-terminal / SMARCC, C-terminal / Histone H2A, C-terminal domain / Histone H2A conserved site / SWI/SNF-like complex subunit BAF250, C-terminal / CENP-T/Histone H4, histone fold / Zinc finger C2H2 superfamily / Winged helix-like DNA-binding domain superfamily / BRCT domain superfamily / ARID DNA-binding domain superfamily / Centromere kinetochore component CENP-T histone fold / SWIB/MDM2 domain superfamily / High mobility group box domain superfamily / BRK domain superfamily / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1 / SWI/SNF complex subunit SMARCC2 / SNF2-like, N-terminal domain superfamily / Core histone H2A/H2B/H3/H4
Histone H3.3 / 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 D member 1 / SWI/SNF complex subunit SMARCC2 / Actin, cytoplasmic 1 / Transcription activator BRG1 / Histone H2A type 1 / Actin-like protein 6A / AT-rich interactive domain-containing protein 1A / Histone H2B ...Histone H3.3 / 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 D member 1 / SWI/SNF complex subunit SMARCC2 / Actin, cytoplasmic 1 / Transcription activator BRG1 / Histone H2A type 1 / Actin-like protein 6A / AT-rich interactive domain-containing protein 1A / Histone H2B / Zinc finger protein ubi-d4 / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1 / Histone H4
Biological speciesXenopus laevis (African clawed frog)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single 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, BAF and PBAF, regulate chromatin structure and transcription, with their mutations linked to cancers. The 3.7 Å-resolution cryo-EM structure of human ...Mammalian SWI/SNF family chromatin remodelers, BAF and PBAF, regulate chromatin structure and transcription, with their mutations linked to cancers. The 3.7 Å-resolution cryo-EM structure of human BAF bound to nucleosome reveals that the nucleosome is sandwiched by the Base and the 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, would engage with and pump 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 nucleosome. ARID1A and 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 Report
SummaryFull reportAbout validation report
History
DepositionJan 22, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release

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Structure visualization

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Assembly

Deposited unit
A: Histone H3.3
B: Histone H4
C: Histone H2A type 1
D: Histone H2B
E: Histone H3.3
F: Histone H4
G: Histone H2A type 1
H: Histone H2B
I: Transcription activator BRG1
J: Actin-like protein 6A
K: Actin, cytoplasmic 1
L: AT-rich interactive domain-containing protein 1A
M: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1
N: SWI/SNF complex subunit SMARCC2
O: SWI/SNF complex subunit SMARCC2
P: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1
Q: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1
R: Zinc finger protein ubi-d4
X: DNA (119-MER)
Y: DNA (119-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,038,93321
Polymers1,038,86820
Non-polymers651
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 10 types, 15 molecules AEBFCGDHIJKLNOR

#1: Protein Histone H3.3 / H3F3A


Mass: 15360.983 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q6PI79
#2: Protein Histone H4 /


Mass: 11394.426 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P62799
#3: Protein Histone H2A type 1


Mass: 13993.295 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P06897
#4: Protein Histone H2B /


Mass: 13873.086 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: H2B / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q92131
#5: Protein Transcription activator BRG1 / ATP-dependent helicase SMARCA4 / BRG1-associated factor 190A / BAF190A


Mass: 184923.828 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMARCA4 / Cell line (production host): HEK293T / Production host: Homo sapiens (human)
References: UniProt: P51532, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#6: Protein Actin-like protein 6A / Actin-related protein Baf53a / ArpNbeta / BRG1-associated factor 53A / BAF53A


Mass: 45236.273 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACTL6A, BAF53, BAF53A / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: O96019
#7: Protein Actin, cytoplasmic 1 / / Beta-actin


Mass: 41782.660 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACTB / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: P60709
#8: Protein AT-rich interactive domain-containing protein 1A / ARID domain-containing protein 1A / B120 / BRG1-associated factor 250 / BAF250 / BRG1-associated ...ARID domain-containing protein 1A / B120 / BRG1-associated factor 250 / BAF250 / BRG1-associated factor 250a / BAF250A


Mass: 142316.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARID1A, BAF250, BAF250A / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: O14497
#10: Protein SWI/SNF complex subunit SMARCC2 / / BRG1-associated factor 170 / BAF170


Mass: 133048.109 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMARCC2 / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q8TAQ2
#13: Protein Zinc finger protein ubi-d4 / / Apoptosis response zinc finger protein / BRG1-associated factor 45D / BAF45D


Mass: 32781.926 Da / Num. of mol.: 1 / Fragment: UNP residues 1-100, UNP residues 209-391
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DPF2, BAF45D / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q92785

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SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily ... , 3 types, 3 molecules MPQ

#9: Protein SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1 / BRG1-associated factor 47 / BAF47


Mass: 38015.094 Da / Num. of mol.: 1 / Fragment: UNP residues 1-113, UNP residues 172-385
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMARCB1, BAF47 / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q12824
#11: Protein SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1


Mass: 58311.391 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMARCD1 / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q96GM5
#12: Protein SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1


Mass: 46710.371 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMARCE1 / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q969G3

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DNA chain , 2 types, 2 molecules XY

#14: DNA chain DNA (119-MER)


Mass: 36520.266 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#15: DNA chain DNA (119-MER)


Mass: 36929.520 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 1 types, 1 molecules

#16: Chemical ChemComp-ZN / ZINC ION / Zinc


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component

Source: RECOMBINANT / Type: COMPLEX

IDNameEntity IDParent-ID
1Structure of nucleosome-bound human BAF complex1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 150
2Nucleosome1, 2, 3, 4, 14, 151
3BAF5, 6, 7, 8, 9, 10, 11, 12, 131
Molecular weightUnits: KILODALTONS/NANOMETER / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Xenopus calcaratus (Biafran clawed frog)451444
33Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDStrainCell
22Escherichia coli BL21 (bacteria)511693BL21
33Homo sapiens (human)9606HEK293T
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: OTHER
Image recordingElectron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM softwareName: RELION / Version: 3.0.8 / Category: 3D reconstruction
CTF correctionType: NONE
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 320658 / Symmetry type: POINT

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