8IHN | pdb_00008ihn

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

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.37 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

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 
• DOI: https://doi.org/10.1038/s41422-023-00884-2
• Primary Citation of Related Structures:  
  8IHM, 8IHN, 8IHT

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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.
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. [e-mail].
Key Laboratory of Anhui Province for Emerging and Reemerging Infectious Diseases, Hefei, Anhui, China. [e-mail].
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. [e-mail].
Key Laboratory of Anhui Province for Emerging and Reemerging Infectious Diseases, Hefei, Anhui, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 7-mer - A2B1C1D1E1F1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 475.11 kDa 
• Atom Count: 14,611 
• Modeled Residue Count: 1,909 
• Deposited Residue Count: 4,163 
• Unique protein chains: 5

Macromolecules

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 P84233 (Xenopus laevis) Explore P84233  Go to UniProtKB:  P84233

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 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 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 Q04779 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q04779  Go to UniProtKB:  Q04779

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 Q12432 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12432  Go to UniProtKB:  Q12432

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	H [auth L]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA (Subject of Investigation/LOI)	I [auth L]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.37 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-03-20 
Deposition Author(s): Zhang, Y., Gang, C.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-03-20
  Type: Initial release
  
• Version 1.1: 2025-07-23
  Changes: Data collection, Structure summary