8IHN

Cryo-EM structure of the Rpd3S core complex

PDB DOI: https://doi.org/10.2210/pdb8IHN/pdb
EM Map EMD-35450: EMDB EMDataResource

Classification: TRANSCRIPTION
Organism(s): Xenopus laevis, Saccharomyces cerevisiae
Expression System: Escherichia coli
Mutation(s): No

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: 3.37 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: 475.11 kDa
Atom Count: 14,611
Modelled Residue Count: 1,909
Deposited Residue Count: 4,163
Unique protein chains: 5

Macromolecules

Find similar proteins by: Sequence | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3	A	24	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A310TTQ1
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulatory protein SIN3	B [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
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone deacetylase RPD3	C [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
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
RCO1 isoform 1	D [auth M], F [auth O]	684	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for A0A8H4BXB0 (Saccharomyces cerevisiae) Explore A0A8H4BXB0 Go to UniProtKB: A0A8H4BXB0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A8H4BXB0
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Chromatin modification-related protein EAF3	E [auth N], G [auth P]	401	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for A0A8H4F719 (Saccharomyces cerevisiae) Explore A0A8H4F719 Go to UniProtKB: A0A8H4F719
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A8H4F719
Sequence Annotations Expand
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 H [auth L] MOL2 format, chain H [auth L]	H [auth L]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain H [auth L] Interactions & Density Focus chain H [auth L]
CA (Subject of Investigation/LOI) Query on CA Download Ideal Coordinates CCD File SDF format, chain I [auth L] MOL2 format, chain I [auth L]	I [auth L]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain I [auth L] Interactions & Density Focus chain I [auth L]