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- PDB-6uxw: SWI/SNF nucleosome complex with ADP-BeFx -

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Entry
Database: PDB / ID: 6uxw
TitleSWI/SNF nucleosome complex with ADP-BeFx
Components
  • (601 sequence ...) x 2
  • (SWI/SNF chromatin-remodeling complex subunit ...) x 2
  • (Transcription regulatory protein ...) x 3
  • Actin-like protein ARP9
  • Actin-related protein 7
  • Histone H2A type 1
  • Histone H2B 1.1
  • Histone H3.2
  • Histone H4
  • Regulator of Ty1 transposition protein 102
  • SWI/SNF complex subunit SWI3
  • SWI/SNF global transcription activator complex subunit SWP82
  • Unknown protein
KeywordsTRANSCRIPTION/DNA / SWI/SNF / chromatin remodeler / TRANSCRIPTION / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


carbon catabolite activation of transcription from RNA polymerase II promoter / RHO GTPases activate IQGAPs / RHO GTPases Activate WASPs and WAVEs / Regulation of actin dynamics for phagocytic cup formation / positive regulation of cell adhesion involved in single-species biofilm formation / positive regulation of mating type switching / positive regulation of pseudohyphal growth by positive regulation of transcription from RNA polymerase II promoter / positive regulation of invasive growth in response to glucose limitation / aggrephagy / Platelet degranulation ...carbon catabolite activation of transcription from RNA polymerase II promoter / RHO GTPases activate IQGAPs / RHO GTPases Activate WASPs and WAVEs / Regulation of actin dynamics for phagocytic cup formation / positive regulation of cell adhesion involved in single-species biofilm formation / positive regulation of mating type switching / positive regulation of pseudohyphal growth by positive regulation of transcription from RNA polymerase II promoter / positive regulation of invasive growth in response to glucose limitation / aggrephagy / Platelet degranulation / rDNA binding / HDACs deacetylate histones / nucleosome disassembly / DNA strand invasion / RSC-type complex / ATP-dependent chromatin remodeler activity / SWI/SNF complex / nuclear chromosome / NuA4 histone acetyltransferase complex / positive regulation of transcription by RNA polymerase I / anatomical structure morphogenesis / ATP-dependent activity, acting on DNA / nucleosomal DNA binding / helicase activity / maturation of LSU-rRNA / chromosome segregation / transcription elongation by RNA polymerase II / nucleotide-excision repair / transcription coregulator activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / double-strand break repair via homologous recombination / lysine-acetylated histone binding / DNA-templated DNA replication / structural constituent of chromatin / nucleosome / double-strand break repair / nucleosome assembly / chromatin organization / histone binding / RNA polymerase II-specific DNA-binding transcription factor binding / hydrolase activity / transcription cis-regulatory region binding / chromatin remodeling / protein heterodimerization activity / chromatin binding / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / structural molecule activity / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / ATP binding / nucleus / metal ion binding / cytosol
Similarity search - Function
Transcription regulator protein Rtt102 / Rtt102p-like transcription regulator protein / SMARCC, C-terminal / SWIRM-associated region 1 / SNF5/SMARCB1/INI1 / SNF5 / SMARCB1 / INI1 / Glutamine-Leucine-Glutamine, QLQ / QLQ / QLQ domain profile. / QLQ ...Transcription regulator protein Rtt102 / Rtt102p-like transcription regulator protein / 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 / 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 superfamily / SANT domain profile. / 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 / Actin / Actin family / Actin / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / 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 / Centromere kinetochore component CENP-T histone fold / Histone H3 signature 1. / Helicase conserved C-terminal domain / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Homeobox-like domain superfamily / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / ATPase, nucleotide binding domain / Histone-fold / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / helicase superfamily c-terminal domain / 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
ADENOSINE-5'-DIPHOSPHATE / BERYLLIUM TRIFLUORIDE ION / PHOSPHATE ION / DNA / DNA (> 10) / DNA (> 100) / Histone H2B 1.1 / Histone H2A type 1 / SWI/SNF chromatin-remodeling complex subunit SWI1 / SWI/SNF chromatin-remodeling complex subunit SNF5 ...ADENOSINE-5'-DIPHOSPHATE / BERYLLIUM TRIFLUORIDE ION / PHOSPHATE ION / DNA / DNA (> 10) / DNA (> 100) / Histone H2B 1.1 / Histone H2A type 1 / 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 / Regulator of Ty1 transposition protein 102 / Transcription regulatory protein SNF12 / Histone H4 / Histone H3.2 / Actin-like protein ARP9 / Actin-related protein 7
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
Saccharomyces cerevisiae (brewer's yeast)
Saccharomyces cerevisiae S288C (yeast)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8.96 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Structure visualization

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Assembly

Deposited unit
R: Histone H3.2
S: Histone H4
T: Histone H2A type 1
U: Histone H2B 1.1
V: Histone H3.2
W: Histone H4
X: Histone H2A type 1
Y: Histone H2B 1.1
a: 601 sequence bottom strand
b: 601 sequence top strand
P: Actin-related protein 7
Q: Actin-like protein ARP9
Z: Regulator of Ty1 transposition protein 102
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,289,69343
Polymers1,288,03528
Non-polymers1,65715
Water1,54986
1


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

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Components

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Protein , 10 types, 21 molecules RVSWTXUYPQZDEFGJKLNOM

#1: Protein Histone H3.2


Mass: 15303.930 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 (E. coli) / References: UniProt: P84233
#2: Protein Histone H4


Mass: 11263.231 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 (E. coli) / References: UniProt: P62799
#3: Protein Histone H2A type 1


Mass: 13978.241 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 (E. coli) / References: UniProt: P06897
#4: Protein Histone H2B 1.1 / H2B1.1


Mass: 13524.752 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated 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: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P02281
#7: Protein Actin-related protein 7 / Actin-like protein ARP7 / Chromatin structure-remodeling complex protein ARP7 / SWI/SNF complex component ARP7


Mass: 53863.016 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: Q12406
#8: Protein Actin-like protein ARP9 / Chromatin structure-remodeling complex protein ARP9 / SWI/SNF complex component ARP9


Mass: 53131.930 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: Q05123
#9: Protein Regulator of Ty1 transposition protein 102


Mass: 17817.615 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: P53330
#13: 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
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P32591
#16: Protein
Unknown protein


Mass: 5720.042 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c
#17: 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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601 sequence ... , 2 types, 2 molecules ab

#5: DNA chain 601 sequence bottom strand


Mass: 56943.293 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#6: DNA chain 601 sequence top strand


Mass: 61785.359 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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

#10: 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
#14: 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
#15: 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

#11: 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
#12: 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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Non-polymers , 5 types, 101 molecules

#18: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: PO4
#19: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#20: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BeF3
#21: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#22: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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 nucleosome complex with ADP-BeFx / Type: COMPLEX / Entity ID: #1-#17 / Source: NATURAL
Molecular weightUnits: MEGADALTONS / Experimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's 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 supportDetails: unspecified
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 FIELD / 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
9RELION3initial Euler assignment
10RELION3final Euler assignment
11RELION3classification
12RELION33D reconstruction
CTF correctionDetails: CTF amplitude correction was performed following 3D auto refinement in relion.
Type: PHASE FLIPPING ONLY
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 8.96 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 35214 / Symmetry type: POINT
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
14I6M

4i6m

14I6M1PDBexperimental model
25Z3V

5z3v

15Z3V2PDBexperimental model
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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