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- PDB-23il: Cryo-EM structure of Chaetomium thermophilum SWI/SNF bound to a n... -

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Basic information

Entry
Database: PDB / ID: 23il
TitleCryo-EM structure of Chaetomium thermophilum SWI/SNF bound to a nucleosome
Components
  • (DNA (167-MER)) x 2
  • ARID domain-containing protein
  • Actin-related protein 4
  • DM2 domain-containing protein
  • DUF1750-domain-containing protein
  • Histone H2A
  • Histone H2B
  • Histone H3
  • Histone H4
  • LYR family protein
  • Nuclear localization protein
  • Putative chromatin structure remodeling complex protein
  • Snf5
  • Ssr1
  • WD40 repeat-containing protein
KeywordsNUCLEAR PROTEIN/DNA / DNA BINDING PROTEIN / Chromatin remodeling complex / SWI/SNF / nucleosome / NUCLEAR PROTEIN-DNA complex
Function / homology
Function and homology information


RSC-type complex / SWI/SNF complex / nuclear chromosome / helicase activity / chromatin DNA binding / transcription by RNA polymerase II / nucleosomal DNA binding / innate immune response in mucosa / structural constituent of chromatin / nucleosome ...RSC-type complex / SWI/SNF complex / nuclear chromosome / helicase activity / chromatin DNA binding / transcription by RNA polymerase II / nucleosomal DNA binding / innate immune response in mucosa / structural constituent of chromatin / nucleosome / nucleosome assembly / antimicrobial humoral immune response mediated by antimicrobial peptide / heterochromatin formation / histone binding / antibacterial humoral response / chromatin organization / transcription cis-regulatory region binding / chromatin remodeling / protein heterodimerization activity / hydrolase activity / DNA repair / 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 / YjgF/YER057c/UK114 family / Endoribonuclease L-PSP / RutC-like superfamily / 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 / Actin, conserved site / Actins signature 2. / Actin / Actin family / Actin / : / 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 / TATA box binding protein associated factor (TAF), histone-like fold domain / Homeobox-like domain superfamily / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Helicase conserved C-terminal domain / Histone H3 signature 1. / ATPase, nucleotide binding domain / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Histone-fold / 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
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / DNA / DNA (> 10) / DNA (> 100) / Histone H3 / Histone H2B / DM2 domain-containing protein / LYR family protein / ARID domain-containing protein / Uncharacterized protein ...ADENOSINE-5'-DIPHOSPHATE / DNA / DNA (> 10) / DNA (> 100) / Histone H3 / Histone H2B / DM2 domain-containing protein / LYR family protein / ARID domain-containing protein / Uncharacterized protein / Uncharacterized protein / Chromatin structure remodeling complex protein / Actin-related protein 4 / Nuclear localization protein / DUF1750-domain-containing protein / WD40 repeat-containing protein / Histone H4 / Histone H2A
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
Thermochaetoides thermophila DSM 1495 (fungus)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.46 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 7, 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
A: Histone H3
B: Histone H4
C: Histone H2A
D: Histone H2B
E: Histone H3
F: Histone H4
G: Histone H2A
H: Histone H2B
K: WD40 repeat-containing protein
L: Putative chromatin structure remodeling complex protein
M: Actin-related protein 4
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
I: DNA (167-MER)
J: DNA (167-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,191,20722
Polymers1,190,77921
Non-polymers4271
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 , 14 types, 19 molecules AEBFCGDHKLMNOPQRSTU

#1: Protein Histone H3


Mass: 15303.930 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: LOC121398065, LOC108703785, LOC121398067 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A310TTQ1
#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


Mass: 13978.241 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: LOC494591, h2ac14.L, hist1h2aj, hist1h2aj.L / Production host: Escherichia coli (E. coli) / References: UniProt: Q6AZJ8
#4: Protein Histone H2B


Mass: 13848.097 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: LOC108704303 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8J0U496
#5: 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)
Gene: CTHT_0069670 / Production host: Homo sapiens (human) / References: UniProt: G0SHD8
#6: Protein Putative chromatin structure remodeling complex protein / Arp9


Mass: 80291.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: THE C-TERMINAL 6AA CONTAINS 6XHIS TAG
Source: (gene. exp.) Thermochaetoides thermophila DSM 1495 (fungus)
Gene: CTHT_0037900 / Production host: Homo sapiens (human) / References: UniProt: G0S882
#7: Protein Actin-related protein 4


Mass: 52832.340 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: THE C-TERMINAL 6AA CONTAINS 6XHIS TAG
Source: (gene. exp.) Thermochaetoides thermophila DSM 1495 (fungus)
Gene: CTHT_0055020 / Production host: Homo sapiens (human) / References: UniProt: G0SBW4
#8: Protein Ssr1


Mass: 75831.109 Da / Num. of mol.: 2
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)
Gene: CTHT_0034160 / Production host: Homo sapiens (human) / References: UniProt: G0S647
#9: 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 ENCODES A FLAG TAG
Source: (gene. exp.) Thermochaetoides thermophila DSM 1495 (fungus)
Gene: CTHT_0007300 / Production host: Homo sapiens (human) / References: UniProt: G0RYN3
#10: 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 ENCODES A FLAG TAG
Source: (gene. exp.) Thermochaetoides thermophila DSM 1495 (fungus)
Gene: CTHT_0060280 / Production host: Homo sapiens (human) / References: UniProt: G0SEZ9
#11: 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)
Gene: CTHT_0020070 / Production host: Homo sapiens (human) / References: UniProt: G0S385
#12: 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)
Gene: CTHT_0023390 / Production host: Homo sapiens (human) / References: UniProt: G0S4S8
#13: 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)
Gene: CTHT_0060030 / Production host: Homo sapiens (human) / References: UniProt: G0SEX4
#14: 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)
Gene: CTHT_0012300 / Production host: Homo sapiens (human) / References: UniProt: G0S145

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DNA chain , 2 types, 2 molecules IJ

#15: DNA chain DNA (167-MER)


Mass: 51333.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#16: DNA chain DNA (167-MER)


Mass: 51773.973 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)

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Non-polymers , 1 types, 1 molecules

#17: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM

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Details

Has ligand of interestY
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: #1-#16 / Source: RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Thermochaetoides thermophila (fungus)209285
31Xenopus laevis (African clawed frog)8355
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
31Escherichia coli (E. coli)562
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
2PHENIXmodel refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 761943
3D reconstructionResolution: 3.46 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 108901 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
RefinementHighest resolution: 3.46 Å / Cross valid method: NONE
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00443000
ELECTRON MICROSCOPYf_angle_d0.76659276
ELECTRON MICROSCOPYf_dihedral_angle_d21.8837907
ELECTRON MICROSCOPYf_chiral_restr0.0426553
ELECTRON MICROSCOPYf_plane_restr0.0056756

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