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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 CDH1 Gene Transcription / positive regulation of glucose mediated signaling pathway / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / positive regulation of norepinephrine uptake / Formation of the polybromo-BAF (pBAF) complex / Formation of the embryonic stem cell BAF (esBAF) complex / Formation of the canonical BAF (cBAF) complex ...negative regulation of myeloid progenitor cell differentiation / single stranded viral RNA replication via double stranded DNA intermediate / Positive Regulation of CDH1 Gene Transcription / positive regulation of glucose mediated signaling pathway / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / positive regulation of norepinephrine uptake / Formation of the polybromo-BAF (pBAF) complex / Formation of the embryonic stem cell BAF (esBAF) complex / Formation of the canonical BAF (cBAF) complex / Formation of neuronal progenitor and neuronal BAF (npBAF and nBAF) / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / Regulation of CDH1 Function / bBAF complex / cellular response to cytochalasin B / Formation of the non-canonical BAF (ncBAF) complex / neural retina development / npBAF complex / brahma complex / nBAF complex / negative regulation of androgen receptor signaling pathway / blastocyst hatching / regulation of transepithelial transport / EGR2 and SOX10-mediated initiation of Schwann cell myelination / hepatocyte differentiation / N-acetyltransferase activity / histone H3K14ac reader activity / morphogenesis of a polarized epithelium / Formation of annular gap junctions / Formation of the dystrophin-glycoprotein complex (DGC) / structural constituent of postsynaptic actin cytoskeleton / Gap junction degradation / Folding of actin by CCT/TriC / GBAF complex / Cell-extracellular matrix interactions / regulation of G0 to G1 transition / protein localization to adherens junction / nucleosome array spacer activity / dense body / Tat protein binding / postsynaptic actin cytoskeleton / RNA polymerase I preinitiation complex assembly / Ino80 complex / Prefoldin mediated transfer of substrate to CCT/TriC / RSC-type complex / blastocyst formation / cellular response to fatty acid / host-mediated activation of viral transcription / XY body / ATP-dependent chromatin remodeler activity / regulation of double-strand break repair / regulation of nucleotide-excision repair / Adherens junctions interactions / RHOF GTPase cycle / adherens junction assembly / nucleosome disassembly / apical protein localization / germ cell nucleus / Sensory processing of sound by outer hair cells of the cochlea / Interaction between L1 and Ankyrins / regulation of mitotic metaphase/anaphase transition / tight junction / SWI/SNF complex / Sensory processing of sound by inner hair cells of the cochlea / positive regulation of T cell differentiation / nuclear androgen receptor binding / apical junction complex / nuclear chromosome / positive regulation of double-strand break repair / spinal cord development / regulation of chromosome organization / regulation of norepinephrine uptake / transporter regulator activity / maintenance of blood-brain barrier / positive regulation of stem cell population maintenance / NuA4 histone acetyltransferase complex / establishment or maintenance of cell polarity / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / cortical cytoskeleton / Recycling pathway of L1 / Regulation of MITF-M-dependent genes involved in pigmentation / regulation of DNA replication / nitric-oxide synthase binding / brush border / regulation of G1/S transition of mitotic cell cycle / regulation of embryonic development / EPH-ephrin mediated repulsion of cells / histone H4K16ac reader activity / negative regulation of cell differentiation / RHO GTPases Activate WASPs and WAVEs / regulation of synaptic vesicle endocytosis / positive regulation of myoblast differentiation / kinesin binding / positive regulation of signal transduction by p53 class mediator / ATP-dependent activity, acting on DNA / positive regulation of Wnt signaling pathway / regulation of DNA repair / RHO GTPases activate IQGAPs / regulation of protein localization to plasma membrane / positive regulation of double-strand break repair via homologous recombination
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 / Snf2-ATP coupling, chromatin remodelling complex / Snf2, ATP coupling domain / Snf2-ATP coupling, chromatin remodelling complex / domain in helicases and associated with SANT domains / HSA 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 / ARID/BRIGHT DNA binding domain / Helicase/SANT-associated domain / HSA domain profile. / SWIRM domain / SWIRM domain / SWIRM domain profile. / SWIB/MDM2 domain / SWIB/MDM2 domain / SWIB/MDM2 domain profile. / SWIB/MDM2 domain superfamily / HMG (high mobility group) box / SANT domain profile. / Histone, subunit A / Chromo/chromo shadow domain / Chromatin organization modifier domain / SANT domain / HMG boxes A and B DNA-binding domains profile. / high mobility group / Histone, subunit A / High mobility group box domain / High mobility group box domain superfamily / Myb-like DNA-binding domain / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / zinc finger / PHD-finger / BRCT domain superfamily / Actins signature 1. / Zinc finger C2H2 type domain profile. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Zinc finger C2H2 superfamily / Zinc finger PHD-type signature. / Actin / Zinc finger C2H2 type domain signature. / Actin family / Actin / Zinc finger PHD-type profile. / Zinc finger C2H2-type / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / : / 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
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 / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 4 / 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 / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 4 / 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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