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- PDB-6uxv: SWI/SNF Body Module -

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Basic information

Entry
Database: PDB / ID: 6uxv
TitleSWI/SNF Body Module
Components
  • (SWI/SNF chromatin-remodeling complex subunit ...) x 2
  • (Transcription regulatory protein ...) x 3
  • (Unknown protein) x 4
  • SWI/SNF complex subunit SWI3
  • SWI/SNF global transcription activator complex subunit SWP82
KeywordsTRANSCRIPTION / SWI/SNF / chromatin remodeler
Function / homology
Function and homology information


carbon catabolite activation of transcription from RNA polymerase II promoter / positive regulation of cell adhesion involved in single-species biofilm formation / positive regulation of mating type switching / positive regulation of invasive growth in response to glucose limitation / HDACs deacetylate histones / aggrephagy / DNA strand invasion / rDNA binding / SWI/SNF complex / ATP-dependent chromatin remodeler activity ...carbon catabolite activation of transcription from RNA polymerase II promoter / positive regulation of cell adhesion involved in single-species biofilm formation / positive regulation of mating type switching / positive regulation of invasive growth in response to glucose limitation / HDACs deacetylate histones / aggrephagy / DNA strand invasion / rDNA binding / SWI/SNF complex / ATP-dependent chromatin remodeler activity / nucleosomal DNA binding / nuclear chromosome / positive regulation of transcription by RNA polymerase I / ATP-dependent activity, acting on DNA / maturation of LSU-rRNA / helicase activity / nucleotide-excision repair / double-strand break repair via homologous recombination / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / lysine-acetylated histone binding / DNA-templated DNA replication / double-strand break repair / histone binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription cis-regulatory region binding / hydrolase activity / chromatin remodeling / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / ATP binding / metal ion binding / nucleus / cytosol
Similarity search - Function
SMARCC, C-terminal / SWIRM-associated region 1 / SNF5/SMARCB1/INI1 / SNF5 / SMARCB1 / INI1 / Glutamine-Leucine-Glutamine, QLQ / QLQ / QLQ domain profile. / QLQ / Snf2, ATP coupling domain / Snf2-ATP coupling, chromatin remodelling complex ...SMARCC, C-terminal / SWIRM-associated region 1 / SNF5/SMARCB1/INI1 / SNF5 / SMARCB1 / INI1 / Glutamine-Leucine-Glutamine, QLQ / QLQ / QLQ domain profile. / QLQ / Snf2, ATP coupling domain / Snf2-ATP coupling, chromatin remodelling complex / Snf2-ATP coupling, chromatin remodelling complex / HSA domain / DNA binding domain with preference for A/T rich regions / Helicase/SANT-associated domain / HSA domain profile. / AT hook, DNA-binding motif / ARID/BRIGHT DNA binding domain / SWIRM domain / SWIRM domain / SWIRM domain profile. / 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 / SANT domain profile. / SWIB/MDM2 domain superfamily / SANT domain / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Myb-like DNA-binding domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / Helicase conserved C-terminal domain / Homeobox-like domain superfamily / Bromodomain, conserved site / Bromodomain signature. / helicase superfamily c-terminal domain / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
SWI/SNF chromatin-remodeling complex subunit SWI1 / SWI/SNF chromatin-remodeling complex subunit SNF5 / Transcription regulatory protein SNF6 / Transcription regulatory protein SNF2 / SWI/SNF complex subunit SWI3 / Transcription regulatory protein SNF12
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Saccharomyces cerevisiae S288C (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.7 Å
AuthorsHe, Y. / Han, Y.
Funding support United States, 3items
OrganizationGrant numberCountry
American Cancer SocietyIRG-15-173-21 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P01 CA092584 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)U54CA193419 United States
CitationJournal: Nature / Year: 2020
Title: Cryo-EM structure of SWI/SNF complex bound to a nucleosome.
Authors: Yan Han / Alexis A Reyes / Sara Malik / Yuan He /
Abstract: The chromatin-remodelling complex SWI/SNF is highly conserved and has critical roles in various cellular processes, including transcription and DNA-damage repair. It hydrolyses ATP to remodel ...The chromatin-remodelling complex SWI/SNF is highly conserved and has critical roles in various cellular processes, including transcription and DNA-damage repair. It hydrolyses ATP to remodel chromatin structure by sliding and evicting histone octamers, creating DNA regions that become accessible to other essential factors. However, our mechanistic understanding of the remodelling activity is hindered by the lack of a high-resolution structure of complexes from this family. Here we report the cryo-electron microscopy structure of Saccharomyces cerevisiae SWI/SNF bound to a nucleosome, at near-atomic resolution. In the structure, the actin-related protein (Arp) module is sandwiched between the ATPase and the rest of the complex, with the Snf2 helicase-SANT associated (HSA) domain connecting all modules. The body contains an assembly scaffold composed of conserved subunits Snf12 (also known as SMARCD or BAF60), Snf5 (also known as SMARCB1, BAF47 or INI1) and an asymmetric dimer of Swi3 (also known as SMARCC, BAF155 or BAF170). Another conserved subunit, Swi1 (also known as ARID1 or BAF250), resides in the core of SWI/SNF, acting as a molecular hub. We also observed interactions between Snf5 and the histones at the acidic patch, which could serve as an anchor during active DNA translocation. Our structure enables us to map and rationalize a subset of cancer-related mutations in the human SWI/SNF complex and to propose a model for how SWI/SNF recognizes and remodels the +1 nucleosome to generate nucleosome-depleted regions during gene activation.
History
DepositionNov 8, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
A: Transcription regulatory protein SNF2
B: SWI/SNF chromatin-remodeling complex subunit SWI1
C: SWI/SNF chromatin-remodeling complex subunit SNF5
D: SWI/SNF complex subunit SWI3
E: SWI/SNF complex subunit SWI3
F: SWI/SNF complex subunit SWI3
G: SWI/SNF complex subunit SWI3
H: Transcription regulatory protein SNF12
I: Transcription regulatory protein SNF6
J: Unknown protein
K: Unknown protein
L: Unknown protein
M: SWI/SNF global transcription activator complex subunit SWP82
N: Unknown protein
O: Unknown protein


Theoretical massNumber of molelcules
Total (without water)921,54615
Polymers921,54615
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Transcription regulatory protein ... , 3 types, 3 molecules AHI

#1: Protein Transcription regulatory protein SNF2 / ATP-dependent helicase SNF2 / Regulatory protein GAM1 / Regulatory protein SWI2 / SWI/SNF complex ...ATP-dependent helicase SNF2 / Regulatory protein GAM1 / Regulatory protein SWI2 / SWI/SNF complex component SNF2 / Transcription factor TYE3


Mass: 194315.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
References: UniProt: P22082, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#5: Protein Transcription regulatory protein SNF12 / SWI/SNF complex component SWP73


Mass: 63947.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P53628
#6: Protein Transcription regulatory protein SNF6 / SWI/SNF complex component SNF6


Mass: 19565.189 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast), (natural) Saccharomyces cerevisiae S288C (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P18888

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SWI/SNF chromatin-remodeling complex subunit ... , 2 types, 2 molecules BC

#2: Protein SWI/SNF chromatin-remodeling complex subunit SWI1 / Regulatory protein GAM3 / SWI/SNF complex subunit SWI1 / Transcription regulatory protein ADR6 / ...Regulatory protein GAM3 / SWI/SNF complex subunit SWI1 / Transcription regulatory protein ADR6 / Transcription regulatory protein SWI1


Mass: 148065.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P09547
#3: Protein SWI/SNF chromatin-remodeling complex subunit SNF5 / SWI/SNF complex subunit SNF5 / Transcription factor TYE4 / Transcription regulatory protein SNF5


Mass: 102642.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P18480

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Protein , 3 types, 6 molecules DEFGJM

#4: Protein
SWI/SNF complex subunit SWI3 / / Transcription factor TYE2 / Transcription regulatory protein SWI3


Mass: 93034.164 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Details: Residues 597-653 and 765-780 of chain F, and residues 609-655 and 763-779 of chain G are not confidently assigned
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P32591
#7: Protein Unknown protein


Mass: 5720.042 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c
#10: Protein SWI/SNF global transcription activator complex subunit SWP82


Mass: 7081.720 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c

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Protein/peptide , 3 types, 4 molecules KLON

#8: Protein/peptide Unknown protein


Mass: 2400.951 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c
#9: Protein/peptide Unknown protein


Mass: 1549.902 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c
#11: Protein/peptide Unknown protein


Mass: 2571.161 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c

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Details

Sequence detailsThe following sequence corresponds to the unknown residue from 151 to the C-terminus for entity-6: ...The following sequence corresponds to the unknown residue from 151 to the C-terminus for entity-6: EMKTQAAELQEKPLTPLKYTKLIAAAEDGSRSTKDMIDAVFEQDSHLRYQPDGVVVHRDDPALVGKLRGDLREAPADYWTHAYRDVLAQYHEAKERIRQKEVTAGEAQDEASLQQQQQQDLQQQQQVVTTVASQSPHATATEKEPVPAVVDDPLENMFGDYSNEPFNTNFDDEFGDLDAVFF This is the actual sequence of Swp82 (entity-10): MLGEDEGNTVLEKGNNPSVKQGEVGAVFIVPKILIREHERVILKQILQILDQDELVQPPLDKFPYKKLELPKYIDELKTR DATNTSYKMIQLDAYGEKKVGSNGELFGGRHYLFNTFTFTAHMGVLLVLLQDVIKVLYQSNATHDEDEFIVQHDQILVME TSEEQTKFLAKNGVIPEESKGSFKYITARSAFVEFGASVIAGGQRIVDDYWESLAKKQNLSSHQRVFKLSTNLISKISLL RPSFQNNRISNANEISANTNNTCTISTSKFESQYPIVTEQPSAEIREAYIENFAKGEHISAIVPGQSISGTLELSAQFRV PRYHSKNSFQQALQMKAMDIPIGRHEELLAQYESQAPDGSASISLPNHIPSVNPSNKPIKRMLSSILDINVSSSKNKKSE ENEMIKPMNKGQHKNNTSLNINGWKFESLPLKSAENSGKQQYYRGLPLYEKNTLLERLKQLTPNEIKELEHLHDAVFVNT GLQNVRKVRTKKWKKYWQYKAGIPIGLKRSQLDEFKNKYLKDVLAQTSVTTNFNEITNTDETITTKRVPNPNFLGNCNIK DFKPPYIYSHVNKVPQNVAGDKTAVKLDTEVKNTNANPVVATDPVAAKPDNLANFSNEVAMNN

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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

ComponentName: SWI/SNF Body module / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightUnits: MEGADALTONS / Experimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Buffer solutionpH: 7.9
Details: 10 mM HEPES, pH 7.9, 10 mM MgCl2, 50 mM KCl, 1 mM DTT, 5% glycerol, 0.05% NP-40
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R3.5/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

MicroscopyModel: JEOL 3200FS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN
Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Image recordingElectron dose: 76.5 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.15.2_3472: / Classification: refinement
EM software
IDNameVersionCategory
2Leginon3.2image acquisition
4Gctf0.5CTF correction
10RELION3initial Euler assignment
11RELION3final Euler assignment
12RELION3classification
13RELION33D reconstruction
CTF correctionDetails: CTF amplitude correction was performed following 3D auto refinement in relion.
Type: PHASE FLIPPING ONLY
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 61518 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00616924
ELECTRON MICROSCOPYf_angle_d0.77722956
ELECTRON MICROSCOPYf_dihedral_angle_d5.66710401
ELECTRON MICROSCOPYf_chiral_restr0.0412687
ELECTRON MICROSCOPYf_plane_restr0.0053000

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