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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 H3.3
  • 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


negative regulation of myeloid progenitor cell differentiation / single stranded viral RNA replication via double stranded DNA intermediate / positive regulation of glucose mediated signaling pathway / H3K9me3 modified histone binding / positive regulation of norepinephrine uptake / cellular response to cytochalasin B / nuclear receptor-mediated glucocorticoid signaling pathway / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / regulation of transepithelial transport ...negative regulation of myeloid progenitor cell differentiation / single stranded viral RNA replication via double stranded DNA intermediate / positive regulation of glucose mediated signaling pathway / H3K9me3 modified histone binding / positive regulation of norepinephrine uptake / cellular response to cytochalasin B / nuclear receptor-mediated glucocorticoid signaling pathway / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / regulation of transepithelial transport / blastocyst hatching / morphogenesis of a polarized epithelium / bBAF complex / postsynaptic actin cytoskeleton organization / negative regulation of androgen receptor signaling pathway / npBAF complex / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / nBAF complex / protein localization to adherens junction / brahma complex / postsynaptic actin cytoskeleton / Tat protein binding / structural constituent of postsynaptic actin cytoskeleton / GBAF complex / dense body / Formation of annular gap junctions / regulation of G0 to G1 transition / neural retina development / Gap junction degradation / EGR2 and SOX10-mediated initiation of Schwann cell myelination / Cell-extracellular matrix interactions / Folding of actin by CCT/TriC / apical protein localization / hepatocyte differentiation / regulation of double-strand break repair / adherens junction assembly / regulation of nucleotide-excision repair / Ino80 complex / XY body / Prefoldin mediated transfer of substrate to CCT/TriC / RSC-type complex / blastocyst formation / RNA polymerase I preinitiation complex assembly / RHOF GTPase cycle / Regulation of MITF-M-dependent genes involved in pigmentation / N-acetyltransferase activity / Adherens junctions interactions / tight junction / positive regulation by host of viral transcription / Sensory processing of sound by outer hair cells of the cochlea / regulation of norepinephrine uptake / Interaction between L1 and Ankyrins / Sensory processing of sound by inner hair cells of the cochlea / regulation of mitotic metaphase/anaphase transition / SWI/SNF complex / nucleosome disassembly / ATP-dependent chromatin remodeler activity / germ cell nucleus / positive regulation of double-strand break repair / regulation of synaptic vesicle endocytosis / positive regulation of T cell differentiation / apical junction complex / cellular response to fatty acid / nuclear androgen receptor binding / establishment or maintenance of cell polarity / nuclear chromosome / regulation of cyclin-dependent protein serine/threonine kinase activity / spinal cord development / maintenance of blood-brain barrier / cortical cytoskeleton / regulation of chromosome organization / positive regulation of stem cell population maintenance / NuA4 histone acetyltransferase complex / nitric-oxide synthase binding / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / regulation of DNA replication / androgen receptor signaling pathway / regulation of G1/S transition of mitotic cell cycle / Recycling pathway of L1 / kinesin binding / brush border / calyx of Held / negative regulation of cell differentiation / regulation of embryonic development / positive regulation of Wnt signaling pathway / positive regulation of double-strand break repair via homologous recombination / EPH-ephrin mediated repulsion of cells / RHO GTPases Activate WASPs and WAVEs / positive regulation of DNA repair / RHO GTPases activate IQGAPs / regulation of protein localization to plasma membrane / estrogen receptor signaling pathway / positive regulation of myoblast differentiation / ATP-dependent activity, acting on DNA / neurogenesis / Chromatin modifying enzymes / regulation of DNA repair / DNA polymerase binding / transcription coregulator activity / lysine-acetylated histone binding
Similarity search - Function
SWI/SNF-like complex subunit BAF250a / SWI/SNF-like complex subunit BAF250/Osa / SWI/SNF-like complex subunit BAF250, C-terminal / SWI/SNF-like complex subunit BAF250/Osa / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1 / SWIB domain / SWI complex, BAF60b domains / DPF1-3, N-terminal domain / SMARCC, SWIRM-associated domain / SMARCC, N-terminal ...SWI/SNF-like complex subunit BAF250a / SWI/SNF-like complex subunit BAF250/Osa / SWI/SNF-like complex subunit BAF250, C-terminal / SWI/SNF-like complex subunit BAF250/Osa / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1 / SWIB domain / SWI complex, BAF60b domains / DPF1-3, N-terminal domain / SMARCC, SWIRM-associated domain / SMARCC, N-terminal / : / : / DPF1-3, N-terminal / SWIRM-associated domain at the N-terminal / SWIRM-associated domain at the C-terminal / MarR-like, BRCT and chromo domains module profile. / : / SWI/SNF Subunit INI1, DNA binding domain / SWI/SNF complex subunit BRG1 / Chromatin-remodeling complex component Sfh1/SNF5 / SMARCC, C-terminal / SWIRM-associated region 1 / SNF5/SMARCB1/INI1 / SNF5 / SMARCB1 / INI1 / BRK domain / BRK domain / BRK domain superfamily / domain in transcription and CHROMO domain helicases / Glutamine-Leucine-Glutamine, QLQ / QLQ / QLQ domain profile. / QLQ / domain in helicases and associated with SANT domains / Snf2, ATP coupling domain / Snf2-ATP coupling, chromatin remodelling complex / Snf2-ATP coupling, chromatin remodelling complex / HSA domain / Helicase/SANT-associated domain / HSA domain profile. / ARID/BRIGHT DNA binding domain / ARID DNA-binding domain / ARID DNA-binding domain superfamily / ARID/BRIGHT DNA binding domain / ARID domain profile. / BRIGHT, ARID (A/T-rich interaction domain) domain / SWIRM domain / SWIRM domain / SWIRM domain profile. / SWIB/MDM2 domain / SWIB/MDM2 domain / SWIB/MDM2 domain profile. / SWIB/MDM2 domain superfamily / SANT domain profile. / SANT domain / HMG (high mobility group) box / Chromo/chromo shadow domain / : / Chromatin organization modifier domain / Histone, subunit A / HMG boxes A and B DNA-binding domains profile. / Histone, subunit A / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / high mobility group / High mobility group box domain / High mobility group box domain superfamily / Myb-like DNA-binding domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / CENP-T/Histone H4, histone fold / zinc finger / Actins signature 1. / Actin, conserved site / Actins signature 2. / Centromere kinetochore component CENP-T histone fold / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Zinc finger C2H2 type domain profile. / Actin / Actin family / Actin / BRCT domain superfamily / Zinc finger C2H2 superfamily / PHD-finger / Zinc finger C2H2 type domain signature. / Zinc finger PHD-type signature. / Zinc finger C2H2-type / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA (> 100) / AT-rich interactive domain-containing protein 1A / Actin-like protein 6A / Histone H2B 1.1 / Histone H2A type 1 / Transcription activator BRG1 / Actin, cytoplasmic 1 / Histone H4 ...DNA / DNA (> 10) / DNA (> 100) / AT-rich interactive domain-containing protein 1A / Actin-like protein 6A / Histone H2B 1.1 / Histone H2A type 1 / Transcription activator BRG1 / Actin, cytoplasmic 1 / Histone H4 / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1 / Histone H3.3 / SWI/SNF complex subunit SMARCC2 / Histone H2B / Zinc finger protein ubi-d4 / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1 / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsHe, S. / Wu, Z. / Tian, Y. / Yu, Z. / Yu, J. / Wang, X. / Li, J. / Liu, B. / Xu, Y.
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.
History
DepositionJan 22, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 25, 2021Group: Database references / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / database_2
Item: _audit_author.name / _citation.journal_volume ..._audit_author.name / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 13, 2021Group: Database references / Category: citation_author / Item: _citation_author.identifier_ORCID
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: cross-linking
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


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, UniProt: P02281*PLUS
#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


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
IDNameTypeEntity IDParent-IDSource
1Structure of nucleosome-bound human BAF complexCOMPLEX#1-#150RECOMBINANT
2NucleosomeCOMPLEX#1-#4, #14-#151RECOMBINANT
3BAFCOMPLEX#5-#131RECOMBINANT
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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