8IHT

Rpd3S bound to the nucleosome

PDB DOI: https://doi.org/10.2210/pdb8IHT/pdb
NAKB: 8IHT
EM Map EMD-35455: EMDB EMDataResource

Classification: TRANSCRIPTION
Organism(s): Xenopus laevis, Saccharomyces cerevisiae
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2023-02-23 Released: 2024-03-20
Deposition Author(s): Zhang, Y., Gang, C.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.72 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 basis for nucleosome binding and catalysis by the yeast Rpd3S/HDAC holoenzyme.

Zhang, Y., Xu, M., Wang, P., Zhou, J., Wang, G., Han, S., Cai, G., Wang, X.

(2023) Cell Res 33: 971-974

PubMed: 37845487 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41422-023-00884-2
Primary Citation of Related Structures:
8IHM, 8IHN, 8IHT

Organizational Affiliation

The First Affiliated Hospital of USTC, MOE Key Laboratory for Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China.

Macromolecule Content

Total Structure Weight: 682.29 kDa
Atom Count: 27,545
Modelled Residue Count: 3,111
Deposited Residue Count: 5,444
Unique protein chains: 8
Unique nucleic acid chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3	A, E	135	Xenopus laevis	Mutation(s): 1 Gene Names: LOC121398065
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
Sequence Annotations Expand
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 Gene Names: LOC121398084
UniProt
Find proteins for P62799 (Xenopus laevis) Explore P62799 Go to UniProtKB: P62799
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% 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: h2ac14.L
UniProt
Find proteins for P06897 (Xenopus laevis) Explore P06897 Go to UniProtKB: P06897
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P06897
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B	D, H	122	Xenopus laevis	Mutation(s): 0 Gene Names: LOC108704303
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: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
RCO1 isoform 1	K [auth M], O	684	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for Q04779 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q04779 Go to UniProtKB: Q04779
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q04779
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Chromatin modification-related protein EAF3	L [auth N], P	401	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for Q12432 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12432 Go to UniProtKB: Q12432
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q12432
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulatory protein SIN3	M [auth K]	1,536	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P22579 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P22579 Go to UniProtKB: P22579
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P22579
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone deacetylase RPD3	N [auth L]	433	Saccharomyces cerevisiae	Mutation(s): 0 EC: 3.5.1.98
UniProt
Find proteins for P32561 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32561 Go to UniProtKB: P32561
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P32561
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Length	Organism	Image
DNA (164-MER)	I	164	Xenopus laevis
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Length	Organism	Image
DNA (165-MER)	J	165	Xenopus laevis
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Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain Q [auth L] MOL2 format, chain Q [auth L]	Q [auth L]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain Q [auth L] Interactions & Density Focus chain Q [auth L]
CA (Subject of Investigation/LOI) Query on CA Download Ideal Coordinates CCD File SDF format, chain R [auth L] MOL2 format, chain R [auth L]	R [auth L]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain R [auth L] Interactions & Density Focus chain R [auth L]