8VRT | pdb_00008vrt

The structure of LSD1-CoREST-HDAC1 in complex with KBTBD4R313PRR mutant


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.42 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

Converging mechanism of UM171 and KBTBD4 neomorphic cancer mutations.

Xie, X.Zhang, O.Yeo, M.J.R.Lee, C.Tao, R.Harry, S.A.Payne, N.C.Nam, E.Paul, L.Li, Y.Kwok, H.S.Jiang, H.Mao, H.Hadley, J.L.Lin, H.Batts, M.Gosavi, P.M.D'Angiolella, V.Cole, P.A.Mazitschek, R.Northcott, P.A.Zheng, N.Liau, B.B.

(2025) Nature 639: 241-249

  • DOI: https://doi.org/10.1038/s41586-024-08533-3
  • Primary Citation of Related Structures:  
    8VPQ, 8VRT, 9DTQ

  • PubMed Abstract: 

    Cancer mutations can create neomorphic protein-protein interactions to drive aberrant function 1,2 . As a substrate receptor of the CULLIN3-RING E3 ubiquitin ligase complex, KBTBD4 is recurrently mutated in medulloblastoma 3 , the most common embryonal brain tumour in children 4 . These mutations impart gain-of-function to KBTBD4 to induce aberrant degradation of the transcriptional corepressor CoREST 5 . However, their mechanism remains unresolved. Here we establish that KBTBD4 mutations promote CoREST degradation through engaging HDAC1/2 as the direct target of the mutant substrate receptor. Using deep mutational scanning, we chart the mutational landscape of the KBTBD4 cancer hotspot, revealing distinct preferences by which insertions and substitutions can promote gain-of-function and the critical residues involved in the hotspot interaction. Cryo-electron microscopy analysis of two distinct KBTBD4 cancer mutants bound to LSD1-HDAC1-CoREST reveals that a KBTBD4 homodimer asymmetrically engages HDAC1 with two KELCH-repeat β-propeller domains. The interface between HDAC1 and one of the KBTBD4 β-propellers is stabilized by the medulloblastoma mutations, which insert a bulky side chain into the HDAC1 active site pocket. Our structural and mutational analyses inform how this hotspot E3-neosubstrate interface can be chemically modulated. First, we unveil a converging shape-complementarity-based mechanism between gain-of-function E3 mutations and a molecular glue degrader, UM171. Second, we demonstrate that HDAC1/2 inhibitors can block the mutant KBTBD4-HDAC1 interface and proliferation of KBTBD4-mutant medulloblastoma cells. Altogether, our work reveals the structural and mechanistic basis of cancer mutation-driven neomorphic protein-protein interactions.


  • Organizational Affiliation
    • Department of Pharmacology, University of Washington, Seattle, WA, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Kelch repeat and BTB domain-containing protein 4
A, B
520Homo sapiensMutation(s): 0 
Gene Names: KBTBD4BKLHD4
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NVX7 (Homo sapiens)
Explore Q9NVX7 
Go to UniProtKB:  Q9NVX7
PHAROS:  Q9NVX7
GTEx:  ENSG00000123444 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NVX7
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone deacetylase 1482Homo sapiensMutation(s): 0 
Gene Names: HDAC1RPD3L1
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 Groups  
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UniProt GroupQ13547
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
REST corepressor 1401Homo sapiensMutation(s): 0 
Gene Names: RCOR1KIAA0071RCOR
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UKL0 (Homo sapiens)
Explore Q9UKL0 
Go to UniProtKB:  Q9UKL0
PHAROS:  Q9UKL0
GTEx:  ENSG00000089902 
Entity Groups  
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UniProt GroupQ9UKL0
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.42 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.1_5286:

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-27
    Type: Initial release
  • Version 1.1: 2025-06-11
    Changes: Data collection, Database references