8IHM | pdb_00008ihm

Eaf3 CHD domain bound to the nucleosome

• PDB DOI: https://doi.org/10.2210/pdb8IHM/pdb
• EM Map EMD-35449: EMDB EMDataResource
• NAKB: 8IHM

• 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: 3.58 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 10-mer - A2B2C2D2E1F1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 10-mer - A6B2C1D1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 8-mer - A2B2C2D2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 8-mer - A2B2C2D2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 225.81 kDa 
• Atom Count: 13,153 
• Modeled Residue Count: 1,202 
• Deposited Residue Count: 1,442 
• Unique protein chains: 6
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3	A, E	135	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
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 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 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 ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Rco1-ABR	K [auth M]	18	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for Q04779 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q04779  Go to UniProtKB:  Q04779

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Chromatin modification-related protein EAF3	L [auth N]	119	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for Q12432 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12432  Go to UniProtKB:  Q12432

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

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

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ML3	A, E	L-PEPTIDE LINKING	C8 H19 N2 O2 S		LYS

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.58 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: 2024-11-06
  Changes: Data collection, Structure summary
• Version 1.2: 2025-07-16
  Changes: Data collection