8VOJ

The Cryo-EM structure of LSD1-CoREST-HDAC1 in complex with KBTBD4 enhanced by UM171 and IP6

• PDB DOI: https://doi.org/10.2210/pdb8VOJ/pdb
• EM Map EMD-43386: EMDB EMDataResource

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


• Deposited: 2024-01-15 Released: 2024-12-04 
• Deposition Author(s): Xie, X., Mao, H., Liau, B., Zheng, N.
• Funding Organization(s): Howard Hughes Medical Institute (HHMI)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.77 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Asymmetric Engagement of Dimeric CRL3KBTBD4 by the Molecular Glue UM171 Licenses Degradation of HDAC1/2 Complexes

Zheng, N., Xie, X., Liau, B.

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: 222.28 kDa 
• Atom Count: 12,109 
• Modelled Residue Count: 1,508 
• Deposited Residue Count: 1,951 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform 2 of Kelch repeat and BTB domain-containing protein 4	A, B	534	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: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone deacetylase 1	C	482	Homo sapiens	Mutation(s): 0  Gene Names: HDAC1, RPD3L1 EC: 3.5.1.98 (PDB Primary Data), 3.5.1 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q13547 (Homo sapiens) Explore Q13547  Go to UniProtKB:  Q13547
PHAROS:  Q13547 GTEx:  ENSG00000116478

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
REST corepressor 1	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IHP	F [auth C]	INOSITOL HEXAKISPHOSPHATE C6 H18 O24 P6 IMQLKJBTEOYOSI-GPIVLXJGSA-N
A1ACV (Subject of Investigation/LOI)	G [auth C]	(1r,4r)-N~1~-[(7P)-2-benzyl-7-(2-methyl-2H-tetrazol-5-yl)-9H-pyrimido[4,5-b]indol-4-yl]cyclohexane-1,4-diamine C25 H27 N9 AZXXGVPWWKWGAE-IYARVYRRSA-N
ZN	E [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.77 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.1_5286:

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-12-04 
Deposition Author(s): Xie, X., Mao, H., 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: 2024-12-04
  Type: Initial release