9C9G | pdb_00009c9g

S.c INO80 in complex with S.c 0/80 nucleosome

PDB DOI: https://doi.org/10.2210/pdb9C9G/pdb
EM Map EMD-45361: EMDB EMDataResource

Classification: DNA BINDING PROTEIN/DNA
Organism(s): Saccharomyces cerevisiae, Xenopus laevis, synthetic construct
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-06-13 Released: 2025-07-16
Deposition Author(s): Wu, H., Kaur, U., Narlikar, G.J., Cheng, Y.F.
Funding Organization(s): National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.91 Å
Aggregation State: CELL
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

Autoinhibition imposed by a large conformational switch of INO80 regulates nucleosome positioning

Kaur, U., Wu, H., Cheng, Y., Narlikar, G.J.

(2025) Science

DOI: https://doi.org/10.1126/science.adr3831

Macromolecule Content

Total Structure Weight: 873.63 kDa
Atom Count: 43,020
Modeled Residue Count: 5,067
Deposited Residue Count: 6,990
Unique protein chains: 10
Unique nucleic acid chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3	A, D [auth E]	136	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: HHT1, YBR010W, YBR0201, HHT2, SIN2, YNL031C, N2749
UniProt
Find proteins for P61830 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P61830 Go to UniProtKB: P61830
Entity Groups
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UniProt Group	P61830
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A.1	B [auth C], E [auth G]	132	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: HTA1, H2A1, SPT11, YDR225W, YD9934.10
UniProt
Find proteins for P04911 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P04911 Go to UniProtKB: P04911
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P04911
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B.1	C [auth D], F [auth H]	131	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: HTB1, H2B1, SPT12, YDR224C, YD9934.09C
UniProt
Find proteins for P02293 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P02293 Go to UniProtKB: P02293
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UniProt Group	P02293
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Chromatin-remodeling ATPase INO80	G [auth Q]	1,489	Saccharomyces cerevisiae	Mutation(s): 0 EC: 3.6.4
UniProt
Find proteins for P53115 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P53115 Go to UniProtKB: P53115
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UniProt Group	P53115
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin-related protein 5	H [auth R]	755	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P53946 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P53946 Go to UniProtKB: P53946
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UniProt Group	P53946
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Chromatin-remodeling complex subunit IES6	I [auth S]	166	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P32617 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32617 Go to UniProtKB: P32617
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UniProt Group	P32617
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
RuvB-like protein 1	J [auth T], L [auth V], N [auth X]	463	Saccharomyces cerevisiae	Mutation(s): 0 EC: 3.6.4.12
UniProt
Find proteins for Q03940 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q03940 Go to UniProtKB: Q03940
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UniProt Group	Q03940
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
RuvB-like protein 2	K [auth U], M [auth W], O [auth Y]	471	Saccharomyces cerevisiae	Mutation(s): 0 EC: 3.6.4.12
UniProt
Find proteins for Q12464 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12464 Go to UniProtKB: Q12464
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UniProt Group	Q12464
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Ino eighty subunit 2	P [auth Z]	320	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P40154 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P40154 Go to UniProtKB: P40154
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UniProt Group	P40154
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	Q [auth B], R [auth F]	103	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: 11
Molecule	Chains	Length	Organism	Image
DNA (227-MER)	S [auth J]	227	synthetic construct
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Reference Sequence

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Entity ID: 12
Molecule	Chains	Length	Organism	Image
DNA (227-MER)	T [auth I]	227	synthetic construct
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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 U] SDF format, chain W [auth V] SDF format, chain X [auth W] SDF format, chain Y [auth X] SDF format, chain Z [auth Y] SDF format, chain U [auth T] MOL2 format, chain V [auth U] MOL2 format, chain W [auth V] MOL2 format, chain X [auth W] MOL2 format, chain Y [auth X] MOL2 format, chain Z [auth Y] MOL2 format, chain U [auth T] mmCIF format, chain V [auth U] mmCIF format, chain W [auth V] mmCIF format, chain X [auth W] mmCIF format, chain Y [auth X] mmCIF format, chain Z [auth Y] mmCIF format, chain U [auth T]	U [auth T] V [auth U] W [auth V] X [auth W] Y [auth X] U [auth T], V [auth U], W [auth V], X [auth W], Y [auth X], Z [auth Y]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain U [auth T] Focus chain V [auth U] Focus chain W [auth V] Focus chain X [auth W] Focus chain Y [auth X] Focus chain Z [auth Y] Interactions & Density Focus chain U [auth T] Focus chain V [auth U] Focus chain W [auth V] Focus chain X [auth W] Focus chain Y [auth X] Focus chain Z [auth Y]