7EGP | pdb_00007egp

The structure of SWI/SNF-nucleosome complex

PDB DOI: https://doi.org/10.2210/pdb7EGP/pdb
EM Map EMD-31137: EMDB EMDataResource
NAKB: 7EGP

Classification: DNA BINDING PROTEIN
Organism(s): Saccharomyces cerevisiae S288C, Xenopus laevis, synthetic construct
Expression System: Escherichia coli-Pichia pastoris shuttle vector pPpARG4
Mutation(s): Yes

Deposited: 2021-03-24 Released: 2022-01-12
Deposition Author(s): Chen, Z.C., Chen, K.J., He, Z.Y., Ye, Y.P.

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 6.90 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Structure of the SWI/SNF complex bound to the nucleosome and insights into the functional modularity.

He, Z.Y., Chen, K.J., Ye, Y.P., Chen, Z.C.

(2021) Cell Discov 7: 28-28

PubMed: 33907182 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41421-021-00262-5
Primary Citation of Related Structures:
7EG6, 7EGM, 7EGP

Organizational Affiliation

Key Laboratory for Protein Sciences of Ministry of Education, School of Life Science, Tsinghua University, Beijing 100084, China.

Macromolecule Content

Total Structure Weight: 1,083.18 kDa
Atom Count: 44,871
Modeled Residue Count: 5,016
Deposited Residue Count: 8,744
Unique protein chains: 14
Unique nucleic acid chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SWI/SNF chromatin-remodeling complex subunit SWI1	A [auth B]	1,093	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: SWI1, ADR6, GAM3, YPL016W, LPA1
UniProt
Find proteins for P09547 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P09547 Go to UniProtKB: P09547
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P09547
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
SWI/SNF chromatin-remodeling complex subunit SNF5	B [auth C]	918	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: SNF5, SWI10, TYE4, YBR289W, YBR2036
UniProt
Find proteins for P18480 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P18480 Go to UniProtKB: P18480
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P18480
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
SWI/SNF complex subunit SWI3	C [auth D], G [auth E]	836	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: SWI3, TYE2, YJL176C, J0495
UniProt
Find proteins for P32591 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32591 Go to UniProtKB: P32591
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P32591
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription regulatory protein SNF12	D [auth H]	566	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: SNF12, SWP73, YNR023W, N3224
UniProt
Find proteins for P53628 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P53628 Go to UniProtKB: P53628
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P53628
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription regulatory protein SNF6	E [auth I]	332	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: SNF6, YHL025W
UniProt
Find proteins for P18888 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P18888 Go to UniProtKB: P18888
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P18888
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
SWI/SNF global transcription activator complex subunit SWP82	F [auth J]	634	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: SWP82, YFL049W
UniProt
Find proteins for P43554 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P43554 Go to UniProtKB: P43554
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P43554
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription regulatory protein SNF2	H [auth A]	982	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: SNF2, GAM1, RIC1, SWI2, TYE3, YOR290C EC: 3.6.4
UniProt
Find proteins for P22082 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P22082 Go to UniProtKB: P22082
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P22082
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Regulator of Ty1 transposition protein 102	I [auth L]	157	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: RTT102, YGR275W, G9378
UniProt
Find proteins for P53330 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P53330 Go to UniProtKB: P53330
Entity Groups
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UniProt Group	P53330
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin-related protein 7	J [auth M]	477	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: ARP7, SWP61, YPR034W, YP9367.14
UniProt
Find proteins for Q12406 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12406 Go to UniProtKB: Q12406
Entity Groups
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UniProt Group	Q12406
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin-like protein ARP9	K [auth N]	467	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: ARP9, SWP59, YMR033W, YM9973.07
UniProt
Find proteins for Q05123 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q05123 Go to UniProtKB: Q05123
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q05123
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Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.2	L [auth O], P [auth S]	135	Xenopus laevis	Mutation(s): 0
UniProt
Find proteins for P84233 (Xenopus laevis) Explore P84233 Go to UniProtKB: P84233
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P84233
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Reference Sequence

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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	M [auth P], Q [auth T]	102	Xenopus laevis	Mutation(s): 0
UniProt
Find proteins for P62799 (Xenopus laevis) Explore P62799 Go to UniProtKB: P62799
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UniProt Group	P62799
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Reference Sequence

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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A	N [auth Q], R [auth U]	129	Xenopus laevis	Mutation(s): 0 Gene Names: hist1h2aj, LOC494591, XELAEV_18003602mg
UniProt
Find proteins for Q6AZJ8 (Xenopus laevis) Explore Q6AZJ8 Go to UniProtKB: Q6AZJ8
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6AZJ8
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Reference Sequence

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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B 1.1	O [auth R], S [auth V]	122	Xenopus laevis	Mutation(s): 1
UniProt
Find proteins for P02281 (Xenopus laevis) Explore P02281 Go to UniProtKB: P02281
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P02281
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Reference Sequence

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Entity ID: 15
Molecule	Chains	Length	Organism	Image
DNA (239-MER)	T [auth W]	235	synthetic construct
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Reference Sequence

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Entity ID: 16
Molecule	Chains	Length	Organism	Image
DNA (239-MER)	U [auth X]	235	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 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 A] MOL2 format, chain V [auth A] mmCIF format, chain V [auth A]	V [auth A]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain V [auth A] Interactions & Density Focus chain V [auth A]
BEF (Subject of Investigation/LOI) Query on BEF Download Ideal Coordinates CCD File SDF format, chain W [auth A] MOL2 format, chain W [auth A] mmCIF format, chain W [auth A]	W [auth A]	BERYLLIUM TRIFLUORIDE ION Be F₃ OGIAHMCCNXDTIE-UHFFFAOYSA-K		Interactions Focus chain W [auth A] Interactions & Density Focus chain W [auth A]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain X [auth A] MOL2 format, chain X [auth A] mmCIF format, chain X [auth A]	X [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain X [auth A] Interactions & Density Focus chain X [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 6.90 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

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Entry History

Deposition Data

Released Date: 2022-01-12

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2022-01-12
Type: Initial release
Version 1.1: 2025-09-17
Changes: Advisory, Data collection, Derived calculations, Structure summary

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.

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.id_divider{ color: #ccc; padding: 0 10px 0 10px; } .extended_id_info{ color: #ccc; font-size: 18px; position: relative; top: -10px; left: 4px; } 7EGP | pdb_00007egp

The structure of SWI/SNF-nucleosome complex

Structure of the SWI/SNF complex bound to the nucleosome and insights into the functional modularity.

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)

7EGP | pdb_00007egp