23IL | pdb_000023il

Cryo-EM structure of Chaetomium thermophilum SWI/SNF bound to a nucleosome

PDB DOI: https://doi.org/10.2210/pdb23IL/pdb
EM Map EMD-68999: EMDB EMDataResource

Classification: NUCLEAR PROTEIN/DNA
Organism(s): Xenopus laevis, Thermochaetoides thermophila DSM 1495, synthetic construct
Expression System: Escherichia coli, Homo sapiens
Mutation(s): No

Deposited: 2026-02-07 Released: 2026-08-12
Deposition Author(s): Ma, S.S., Liu, M.D., Shen, Q.T., Chen, Y.
Funding Organization(s): Ministry of Science and Technology (MoST, China)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.46 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structural principles underlying the evolution of SWI/SNF chromatin remodelers

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.

(2026) Sci Adv

Macromolecule Content

Total Structure Weight: 1,191.21 kDa
Atom Count: 41,626
Modeled Residue Count: 4,774
Deposited Residue Count: 10,259
Unique protein chains: 14
Unique nucleic acid chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3	A, E	135	Xenopus laevis	Mutation(s): 0 Gene Names: LOC121398065, LOC108703785, LOC121398067
UniProt
Find proteins for A0A310TTQ1 (Xenopus laevis) Explore A0A310TTQ1 Go to UniProtKB: A0A310TTQ1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A310TTQ1
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	B, F	102	Xenopus laevis	Mutation(s): 0
UniProt
Find proteins for P62799 (Xenopus laevis) Explore P62799 Go to UniProtKB: P62799
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62799
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A	C, G	129	Xenopus laevis	Mutation(s): 0 Gene Names: LOC494591, h2ac14.L, hist1h2aj, hist1h2aj.L
UniProt
Find proteins for Q6AZJ8 (Xenopus laevis) Explore Q6AZJ8 Go to UniProtKB: Q6AZJ8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6AZJ8
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B	D, H	125	Xenopus laevis	Mutation(s): 0 Gene Names: LOC108704303
UniProt
Find proteins for A0A8J0U496 (Xenopus laevis) Explore A0A8J0U496 Go to UniProtKB: A0A8J0U496
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A8J0U496
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
WD40 repeat-containing protein	I [auth K]	1,595	Thermochaetoides thermophila DSM 1495	Mutation(s): 0 Gene Names: CTHT_0069670
UniProt
Find proteins for G0SHD8 (Thermochaetoides thermophila (strain DSM 1495 / CBS 144.50 / DAOM 24625 / IMI 039719)) Explore G0SHD8 Go to UniProtKB: G0SHD8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G0SHD8
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative chromatin structure remodeling complex protein	J [auth L]	733	Thermochaetoides thermophila DSM 1495	Mutation(s): 0 Gene Names: CTHT_0037900
UniProt
Find proteins for G0S882 (Thermochaetoides thermophila (strain DSM 1495 / CBS 144.50 / DAOM 24625 / IMI 039719)) Explore G0S882 Go to UniProtKB: G0S882
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G0S882
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin-related protein 4	K [auth M]	476	Thermochaetoides thermophila DSM 1495	Mutation(s): 0 Gene Names: CTHT_0055020
UniProt
Find proteins for G0SBW4 (Thermochaetoides thermophila (strain DSM 1495 / CBS 144.50 / DAOM 24625 / IMI 039719)) Explore G0SBW4 Go to UniProtKB: G0SBW4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G0SBW4
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Ssr1	L [auth N], M [auth O]	694	Thermochaetoides thermophila DSM 1495	Mutation(s): 0 Gene Names: CTHT_0034160
UniProt
Find proteins for G0S647 (Thermochaetoides thermophila (strain DSM 1495 / CBS 144.50 / DAOM 24625 / IMI 039719)) Explore G0S647 Go to UniProtKB: G0S647
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G0S647
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
DM2 domain-containing protein	N [auth P]	547	Thermochaetoides thermophila DSM 1495	Mutation(s): 0 Gene Names: CTHT_0007300
UniProt
Find proteins for G0RYN3 (Thermochaetoides thermophila (strain DSM 1495 / CBS 144.50 / DAOM 24625 / IMI 039719)) Explore G0RYN3 Go to UniProtKB: G0RYN3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G0RYN3
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
DUF1750-domain-containing protein	O [auth Q]	769	Thermochaetoides thermophila DSM 1495	Mutation(s): 0 Gene Names: CTHT_0060280
UniProt
Find proteins for G0SEZ9 (Thermochaetoides thermophila (strain DSM 1495 / CBS 144.50 / DAOM 24625 / IMI 039719)) Explore G0SEZ9 Go to UniProtKB: G0SEZ9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G0SEZ9
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Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
ARID domain-containing protein	P [auth R]	1,301	Thermochaetoides thermophila DSM 1495	Mutation(s): 0 Gene Names: CTHT_0020070
UniProt
Find proteins for G0S385 (Thermochaetoides thermophila (strain DSM 1495 / CBS 144.50 / DAOM 24625 / IMI 039719)) Explore G0S385 Go to UniProtKB: G0S385
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G0S385
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Reference Sequence

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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Snf5	Q [auth S]	785	Thermochaetoides thermophila DSM 1495	Mutation(s): 0 Gene Names: CTHT_0023390
UniProt
Find proteins for G0S4S8 (Thermochaetoides thermophila (strain DSM 1495 / CBS 144.50 / DAOM 24625 / IMI 039719)) Explore G0S4S8 Go to UniProtKB: G0S4S8
Entity Groups
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UniProt Group	G0S4S8
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Reference Sequence

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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear localization protein	R [auth T]	722	Thermochaetoides thermophila DSM 1495	Mutation(s): 0 Gene Names: CTHT_0060030
UniProt
Find proteins for G0SEX4 (Thermochaetoides thermophila (strain DSM 1495 / CBS 144.50 / DAOM 24625 / IMI 039719)) Explore G0SEX4 Go to UniProtKB: G0SEX4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G0SEX4
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Reference Sequence

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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
LYR family protein	S [auth U]	627	Thermochaetoides thermophila DSM 1495	Mutation(s): 0 Gene Names: CTHT_0012300
UniProt
Find proteins for G0S145 (Thermochaetoides thermophila (strain DSM 1495 / CBS 144.50 / DAOM 24625 / IMI 039719)) Explore G0S145 Go to UniProtKB: G0S145
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G0S145
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 15
DNA (167-MER)	T [auth I]	167	synthetic construct
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 16
DNA (167-MER)	U [auth J]	167	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP (Subject of Investigation/LOI) Query on ADP Download:Ideal Coordinates CCD File SDF format, chain V [auth K] MOL2 format, chain V [auth K] mmCIF format, chain V [auth K]	V [auth K]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain V [auth K] Interactions & Density Focus chain V [auth K]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.46 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-08-12

Deposition Author(s):

Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2023YFA1800403

Revision History (Full details and data files)

Version 1.0: 2026-08-12
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

23IL | pdb_000023il

Cryo-EM structure of Chaetomium thermophilum SWI/SNF bound to a nucleosome

Literature

Structural principles underlying the evolution of SWI/SNF chromatin remodelers

Biological Assembly 1

Macromolecules

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Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Entry History

Deposition Data

Revision History (Full details and data files)