8IHT | pdb_00008iht

Rpd3S bound to the nucleosome

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 1.2 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

  • 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.

Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3
A, E
135Xenopus laevisMutation(s): 1 
Gene Names: LOC121398065
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Find proteins for P84233 (Xenopus laevis)
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UniProt GroupP84233
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4
B, F
102Xenopus laevisMutation(s): 0 
Gene Names: LOC121398084
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2A
C, G
129Xenopus laevisMutation(s): 0 
Gene Names: h2ac14.L
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B
D, H
122Xenopus laevisMutation(s): 0 
Gene Names: LOC108704303
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
RCO1 isoform 1K [auth M],
O		684Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Chromatin modification-related protein EAF3L [auth N],
P		401Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Transcriptional regulatory protein SIN3M [auth K]1,536Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Histone deacetylase RPD3N [auth L]433Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.5.1.98
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Entity ID: 5
MoleculeChains LengthOrganismImage
DNA (164-MER)164Xenopus laevis
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Entity ID: 6
MoleculeChains LengthOrganismImage
DNA (165-MER)165Xenopus laevis
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Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
ML3
Query on ML3
A, E
L-PEPTIDE LINKINGC8 H19 N2 O2 SLYS
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.72 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-03-20
    Type: Initial release
  • Version 1.1: 2024-10-30
    Changes: Data collection, Structure summary
  • Version 1.2: 2025-07-16
    Changes: Data collection