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- PDB-9pbs: Core SWI/SNF of PIC-Med-SWI/SNF-Nucleosome -

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Basic information

Entry
Database: PDB / ID: 9pbs
TitleCore SWI/SNF of PIC-Med-SWI/SNF-Nucleosome
Components
  • (SWI/SNF chromatin-remodeling complex subunit ...) x 2
  • (Transcription regulatory protein ...) x 3
  • SWI/SNF complex subunit SWI3
  • SWI/SNF global transcription activator complex subunit SWP82
  • Unknown
KeywordsTRANSCRIPTION / SWI/SNF / PIC
Function / homology
Function and homology information


carbon catabolite activation of transcription / 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 / RSC-type complex / SUMOylation of chromatin organization proteins ...carbon catabolite activation of transcription / 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 / RSC-type complex / SUMOylation of chromatin organization proteins / histone H3K14ac reader activity / SWI/SNF complex / ATP-dependent chromatin remodeler activity / double-strand break repair via break-induced replication / nuclear chromosome / positive regulation of transcription by RNA polymerase I / histone H4 reader activity / maturation of LSU-rRNA / histone reader activity / cellular response to amino acid starvation / transcription initiation-coupled chromatin remodeling / chromatin DNA binding / double-strand break repair via homologous recombination / nucleotide-excision repair / DNA-templated DNA replication / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / nucleosomal DNA binding / double-strand break repair / histone binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription cis-regulatory region binding / chromatin remodeling / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / chromatin / structural molecule activity / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / DNA binding / ATP binding / nucleus / cytosol
Similarity search - Function
: / : / Chromatin-remodelling complex, RSC SWI/SNF subunit Rsc7/Swp82 / Chromatin remodelling complex Rsc7/Swp82 subunit / : / SWIFT domain / SMARCC, C-terminal / SWIRM-associated region 1 / SNF5/SMARCB1/INI1 / SNF5 / SMARCB1 / INI1 ...: / : / Chromatin-remodelling complex, RSC SWI/SNF subunit Rsc7/Swp82 / Chromatin remodelling complex Rsc7/Swp82 subunit / : / SWIFT domain / SMARCC, C-terminal / SWIRM-associated region 1 / SNF5/SMARCB1/INI1 / SNF5 / SMARCB1 / INI1 / QLQ / Glutamine-Leucine-Glutamine, QLQ / QLQ domain profile. / QLQ / Snf2-ATP coupling, chromatin remodelling complex / Snf2, ATP coupling domain / Snf2-ATP coupling, chromatin remodelling complex / DNA binding domain with preference for A/T rich regions / AT hook, DNA-binding motif / 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 / SWIRM domain / SWIRM domain / SWIRM domain profile. / Helicase/SANT-associated domain / HSA domain profile. / SWIB/MDM2 domain superfamily / SANT domain profile. / SANT domain / 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 / Homeobox-like domain superfamily / Helicase conserved C-terminal domain / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / 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
SWI/SNF chromatin-remodeling complex subunit SWI1 / SWI/SNF chromatin-remodeling complex subunit SNF5 / Transcription regulatory protein SNF6 / SWI/SNF chromatin-remodeling complex subunit SNF2 / SWI/SNF complex subunit SWI3 / SWI/SNF global transcription activator complex subunit SWP82 / Transcription regulatory protein SNF12
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsYang, C. / Nagai, S. / Chen, D.-H.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: To Be Published
Title: Structure of Core SWI/SNF of PIC-Med-SWI/SNF-Nucleosome
Authors: Yang, C. / Nagai, S. / Chen, D.-H.
History
DepositionJun 26, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2026Provider: repository / Type: Initial release
Revision 1.0Oct 7, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)810,6589
Polymers810,6589
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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

#1: 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 (brewer's yeast) / References: UniProt: P53628
#3: Protein Transcription regulatory protein SNF6 / SWI/SNF complex component SNF6


Mass: 37652.582 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P18888
#7: 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 (brewer's yeast)
References: UniProt: P22082, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement

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Protein , 3 types, 4 molecules BDEG

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


Mass: 93034.164 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32591
#4: Protein SWI/SNF global transcription activator complex subunit SWP82


Mass: 70366.617 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P43554
#6: Protein Unknown


Mass: 7600.243 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)

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

#5: 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 (brewer's yeast) / References: UniProt: P18480
#8: 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 (brewer's yeast) / References: UniProt: P09547

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Details

Has protein modificationY

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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: Core SWI/SNF of PIC-Med-SWI/SNF-Nucleosome / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightValue: 2 MDa / Experimental value: YES
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Buffer solutionpH: 7.5
Details: 40 mM Hepes-KOH pH 7.5, 100 mM potassium acetate, 2 mM magnesium acetate and 5 mM DTT
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 64000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 4 sec. / Electron dose: 40.8 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
1RELION5particle selection
2PHENIX1.20.1_4487model refinement
3SerialEMimage acquisition
13cryoSPARC3D reconstruction
CTF correctionType: NONE
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 121711 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
17egp

7egp

17egp1PDBexperimental model
27c4j

7c4j

17c4j2PDBexperimental model
RefinementStereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0124832
ELECTRON MICROSCOPYf_angle_d1.33533558
ELECTRON MICROSCOPYf_dihedral_angle_d5.6293217
ELECTRON MICROSCOPYf_chiral_restr0.0633782
ELECTRON MICROSCOPYf_plane_restr0.0084307

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