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- PDB-23fj: Cryo-EM structure of SWI/SNF complex from Chaetomium thermophilum -

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Basic information

Entry
Database: PDB / ID: 23fj
TitleCryo-EM structure of SWI/SNF complex from Chaetomium thermophilum
Components
  • ARID domain-containing protein
  • DM2 domain-containing protein
  • DUF1750-domain-containing protein
  • LYR family protein
  • Nuclear localization protein
  • Snf5
  • Ssr1
  • WD40 repeat-containing protein
KeywordsNUCLEAR PROTEIN / DNA BINDING PROTEIN / Chromatin remodeling complex / SWI/SNF / nucleosome
Function / homology
Function and homology information


RSC-type complex / SWI/SNF complex / nuclear chromosome / helicase activity / chromatin DNA binding / transcription by RNA polymerase II / histone binding / transcription cis-regulatory region binding / chromatin remodeling / hydrolase activity ...RSC-type complex / SWI/SNF complex / nuclear chromosome / helicase activity / chromatin DNA binding / transcription by RNA polymerase II / histone binding / transcription cis-regulatory region binding / chromatin remodeling / hydrolase activity / regulation of transcription by RNA polymerase II / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / DNA binding / DNA-templated transcription / ATP binding / nucleus
Similarity search - Function
SWI/SNF and RSC complexes subunit Ssr4, N-terminal / SWI/SNF and RSC complexes subunit Ssr4, C-terminal / SWI/SNF and RSC complexes subunit Ssr4 N-terminal / SWI/SNF and RSC complexes subunit Ssr4 C-terminal / Rsc8/Ssr1/Ssr2, zinc finger, ZZ-type / : / Chromatin-remodelling complex, RSC SWI/SNF subunit Rsc7/Swp82 / Chromatin remodelling complex Rsc7/Swp82 subunit / SWIB domain / SWI complex, BAF60b domains ...SWI/SNF and RSC complexes subunit Ssr4, N-terminal / SWI/SNF and RSC complexes subunit Ssr4, C-terminal / SWI/SNF and RSC complexes subunit Ssr4 N-terminal / SWI/SNF and RSC complexes subunit Ssr4 C-terminal / Rsc8/Ssr1/Ssr2, zinc finger, ZZ-type / : / Chromatin-remodelling complex, RSC SWI/SNF subunit Rsc7/Swp82 / Chromatin remodelling complex Rsc7/Swp82 subunit / SWIB domain / SWI complex, BAF60b domains / SMARCC, C-terminal / SWIRM-associated region 1 / SNF5/SMARCB1/INI1 / SNF5 / SMARCB1 / INI1 / Glutamine-Leucine-Glutamine, QLQ / QLQ domain profile. / QLQ / Myb-like domain profile. / Snf2-ATP coupling, chromatin remodelling complex / Snf2, ATP coupling domain / Snf2-ATP coupling, chromatin remodelling complex / 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. / HSA domain / SWIB/MDM2 domain / SWIB/MDM2 domain / SWIB/MDM2 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 / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / helicase superfamily c-terminal domain / WD domain, G-beta repeat / 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 / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / Winged helix-like DNA-binding domain superfamily / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DM2 domain-containing protein / LYR family protein / ARID domain-containing protein / Uncharacterized protein / Uncharacterized protein / Nuclear localization protein / DUF1750-domain-containing protein / WD40 repeat-containing protein
Similarity search - Component
Biological speciesThermochaetoides thermophila DSM 1495 (fungus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.96 Å
AuthorsMa, S.S. / Liu, M.D. / Shen, Q.T. / Chen, Y.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2023YFA1800403 China
CitationJournal: Sci Adv / Year: 2026
Title: Structural principles underlying the evolution of SWI/SNF chromatin remodelers
Authors: Ma, S.S. / Liu, M.D. / Xu, W.C. / Wang, Q.M. / Wang, X.M. / Huang, Y.G. / Li, M.C. / Li, C.H. / Shen, Q.T. / Chen, Y.
History
DepositionFeb 5, 2026Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 12, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 12, 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
K: WD40 repeat-containing protein
N: Ssr1
O: Ssr1
P: DM2 domain-containing protein
Q: DUF1750-domain-containing protein
R: ARID domain-containing protein
S: Snf5
T: Nuclear localization protein
U: LYR family protein


Theoretical massNumber of molelcules
Total (without water)845,7619
Polymers845,7619
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 8 types, 9 molecules KNOPQRSTU

#1: Protein WD40 repeat-containing protein / Snf2


Mass: 179692.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The N-terminal 62aa contains 3xFlag tag, 3C site, and the cloning linker.
Source: (gene. exp.) Thermochaetoides thermophila DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0069670 / Production host: Homo sapiens (human) / References: UniProt: G0SHD8
#2: Protein Ssr1


Mass: 75831.109 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The C-terminal 8aa encode Flag tag
Source: (gene. exp.) Thermochaetoides thermophila DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0034160 / Production host: Homo sapiens (human) / References: UniProt: G0S647
#3: Protein DM2 domain-containing protein / Ssr3


Mass: 61496.863 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The C-terminal 8aa encode Flag tag
Source: (gene. exp.) Thermochaetoides thermophila DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0007300 / Production host: Homo sapiens (human) / References: UniProt: G0RYN3
#4: Protein DUF1750-domain-containing protein / Ssr4


Mass: 81947.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The C-terminal 8aa encode Flag tag
Source: (gene. exp.) Thermochaetoides thermophila DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0060280 / Production host: Thermochaetoides thermophila (fungus) / References: UniProt: G0SEZ9
#5: Protein ARID domain-containing protein / Sol1


Mass: 140244.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The N-terminal 62aa contains 3xFlag tag, 3C site, and the cloning linker.
Source: (gene. exp.) Thermochaetoides thermophila DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0020070 / Production host: Homo sapiens (human) / References: UniProt: G0S385
#6: Protein Snf5


Mass: 87782.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The C-terminal 8aa encodes a Flag tag
Source: (gene. exp.) Thermochaetoides thermophila DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0023390 / Production host: Homo sapiens (human) / References: UniProt: G0S4S8
#7: Protein Nuclear localization protein / Snf59


Mass: 76208.398 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The C-terminal 8aa encodes a Flag tag
Source: (gene. exp.) Thermochaetoides thermophila DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0060030 / Production host: Homo sapiens (human) / References: UniProt: G0SEX4
#8: Protein LYR family protein / Snf70


Mass: 66726.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The C-terminal 6aa encodes a 6xHis tag
Source: (gene. exp.) Thermochaetoides thermophila DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0012300 / Production host: Homo sapiens (human) / References: UniProt: G0S145

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Details

Has protein modificationN

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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 / Type: COMPLEX
Details: The SWI/SNF complex is overexpressed in 293F cells and purified by affinity chromatography, anion exchange chromatography, Grafix, etc.
Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Thermochaetoides thermophila DSM 1495 (fungus)
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
31Thermochaetoides thermophila (fungus)209285
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
130 mMPotassium chlorideKCl1
22 mMMagnesium chlorideMgCl21
320 mMHEPEsC8H18N2O4S1
40.5 mMADPC10H15N5O10P21
51 mMBeryllium sulfateBeSO41
68 mMsodium fluorideNaF1
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was homogenous and monodisperse.
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: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameCategory
1RELIONparticle selection
7UCSF Chimeramodel fitting
12cryoSPARC3D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 158634 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00319136
ELECTRON MICROSCOPYf_angle_d0.68625877
ELECTRON MICROSCOPYf_dihedral_angle_d5.0172573
ELECTRON MICROSCOPYf_chiral_restr0.0442832
ELECTRON MICROSCOPYf_plane_restr0.0063413

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