8HPO

Cryo-EM structure of a SIN3/HDAC complex from budding yeast


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure of a SIN3-HDAC complex from budding yeast.

Guo, Z.Chu, C.Lu, Y.Zhang, X.Xiao, Y.Wu, M.Gao, S.Wong, C.C.L.Zhan, X.Wang, C.

(2023) Nat Struct Mol Biol 30: 753-760

  • DOI: https://doi.org/10.1038/s41594-023-00975-z
  • Primary Citation of Related Structures:  
    8HPO

  • PubMed Abstract: 

    SIN3-HDAC (histone deacetylases) complexes have important roles in facilitating local histone deacetylation to regulate chromatin accessibility and gene expression. Here, we present the cryo-EM structure of the budding yeast SIN3-HDAC complex Rpd3L at an average resolution of 2.6 Å. The structure reveals that two distinct arms (ARM1 and ARM2) hang on a T-shaped scaffold formed by two coiled-coil domains. In each arm, Sin3 interacts with different subunits to create a different environment for the histone deacetylase Rpd3. ARM1 is in the inhibited state with the active site of Rpd3 blocked, whereas ARM2 is in an open conformation with the active site of Rpd3 exposed to the exterior space. The observed asymmetric architecture of Rpd3L is different from those of available structures of other class I HDAC complexes. Our study reveals the organization mechanism of the SIN3-HDAC complex and provides insights into the interaction pattern by which it targets histone deacetylase to chromatin.


  • Organizational Affiliation

    College of Life Sciences, Zhejiang University, Hangzhou, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transcriptional regulatory protein UME1A [auth K]460Saccharomyces cerevisiae S288CMutation(s): 0 
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UniProt GroupQ03010
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Transcriptional regulatory protein SDS3B [auth D]327Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P40505 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Histone deacetylase RPD3C [auth F]433Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 3.5.1.98
UniProt
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UniProt GroupP32561
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Histone deacetylase RPD3D [auth G]433Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 3.5.1.98
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Transcriptional regulatory protein SAP30E [auth I]201Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Transcriptional regulatory protein SIN3F [auth A],
J [auth B]
1,536Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Transcriptional regulatory protein DEP1G [auth H]405Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Transcriptional regulatory protein PHO23H [auth C]330Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Transcriptional regulatory protein RXT2I [auth E]430Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Transcriptional regulatory protein RXT3K [auth J]294Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TPO
Query on TPO

Download Ideal Coordinates CCD File 
L [auth F]PHOSPHOTHREONINE
C4 H10 N O6 P
USRGIUJOYOXOQJ-GBXIJSLDSA-N
ZN
Query on ZN

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M [auth F],
P [auth G]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K
Query on K

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N [auth F],
O [auth F],
Q [auth G],
R [auth G]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP
B [auth D]L-PEPTIDE LINKINGC3 H8 N O6 PSER
TPO
Query on TPO
C [auth F]L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-03
    Type: Initial release
  • Version 1.1: 2023-07-05
    Changes: Database references