9DTQ

The structure of HDAC2-CoREST in complex with KBTBD4R313PRR mutant

• PDB DOI: https://doi.org/10.2210/pdb9DTQ/pdb
• EM Map EMD-47156: EMDB EMDataResource

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda, Trichoplusia ni, Homo sapiens
• Mutation(s): No 


• Deposited: 2024-10-01 Released: 2024-11-27 
• Deposition Author(s): Xie, X., Liau, B., Zheng, N.
• Funding Organization(s): Howard Hughes Medical Institute (HHMI)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.87 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Molecular Mechanism Underlying KBTBD4 Cancer Mutation-Driven Degradation of HDAC Corepressor Complexes

Xie, X., Liau, B., Zheng, N.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B1C1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 218.87 kDa 
• Atom Count: 12,162 
• Modelled Residue Count: 1,523 
• Deposited Residue Count: 1,928 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone deacetylase 2	A	487	Homo sapiens	Mutation(s): 0  Gene Names: HDAC2 EC: 3.5.1.98 (PDB Primary Data), 3.5.1 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q92769 (Homo sapiens) Explore Q92769  Go to UniProtKB:  Q92769
PHAROS:  Q92769 GTEx:  ENSG00000196591

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Kelch repeat and BTB domain-containing protein 4	B, D [auth E]	520	Homo sapiens	Mutation(s): 0  Gene Names: KBTBD4, BKLHD4
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NVX7 (Homo sapiens) Explore Q9NVX7  Go to UniProtKB:  Q9NVX7
PHAROS:  Q9NVX7 GTEx:  ENSG00000123444

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
REST corepressor 1	C [auth D]	401	Homo sapiens	Mutation(s): 0  Gene Names: RCOR1, KIAA0071, RCOR
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UKL0 (Homo sapiens) Explore Q9UKL0  Go to UniProtKB:  Q9UKL0
PHAROS:  Q9UKL0 GTEx:  ENSG00000089902

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IHP (Subject of Investigation/LOI)	E [auth D]	INOSITOL HEXAKISPHOSPHATE C6 H18 O24 P6 IMQLKJBTEOYOSI-GPIVLXJGSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.87 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21_5207:

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-11-27 
Deposition Author(s): Xie, X., Liau, B., Zheng, N.

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Funding Organization	Location	Grant Number
Howard Hughes Medical Institute (HHMI)	United States	--

Revision History  

• Version 1.0: 2024-11-27
  Type: Initial release