9Y61 | pdb_00009y61

Cryo-EM structure of ternary complex NSD2-PWWP1:CRBN:DDB1 in complex with NSD2-LDD, an LDD degrader


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9Y61

This is version 1.0 of the entry. See complete history

Literature

NSD2 Degradation Remediates the Oncogenic Cistrome in t(4;14) Multiple Myeloma.

Hu, B.Edwards, J.Modi, H.Gamez, J.Echeagaray, O.E.Hess, K.Ren, Y.Anderson, D.Larrayoz, M.Zhu, J.Johnson, S.A.Deb, G.Jankeel, D.Janardhanan, P.Leisten, J.Peng, S.Christoforou, A.Stong, N.Fontanillo, C.Bjorklund, C.C.Hagner, P.R.Gandhi, A.K.Martinez-Climent, J.A.Narla, R.K.Lopez-Girona, A.Rolfe, M.Bence, N.Mortensen, D.S.Groocock, L.

(2026) Blood 

  • DOI: https://doi.org/10.1182/blood.2025031998
  • Primary Citation Related Structures: 
    9Y60, 9Y61

  • PubMed Abstract: 

    The t(4;14) chromosomal translocation drives overexpression of the histone methyltransferase NSD2 and defines a high-risk segment of multiple myeloma (MM) patients. Herein, we report the discovery of NSD2-LDD, a cereblon-recruiting and PWWP1-mediated ligand directed degrader (LDD) that selectively and potently eliminates full length and PWWP1 domain containing NSD2 protein isoforms. NSD2-LDD treatment induces global loss of H3K36me2 leading to promoter-proximal spreading of H3K27me3 and re-wiring of cis-regulatory interactions that reverse t(4;14) transcriptional programs. These effects suppress MM disease-associated phenotypes including stromal adhesion, three-dimensional colony growth and paracrine signaling. By integrating patient single cell profiles with model 3D epigenomic and spatial transcriptomics, we delineate t(4;14) disease state together with the tumor-intrinsic reprogramming and resultant remodeling of the bone marrow microenvironment upon NSD2 degradation. In cell line derived xenografts and genetically engineered mouse models of t(4;14), NSD2-LDD extends median survival accompanied by tumoral H3K36me2 loss and niche re-modelling. Although the NSD2-LDD response is restricted to PWWP1-containining models, collectively this work validates NSD2 as a tractable dependency and supports clinical development of NSD2 degradation as a novel, targeted therapeutic strategy in high-risk MM.


  • Organizational Affiliation
    • Bristol Myers Squibb, San Diego, California, United States.

Macromolecule Content 

  • Total Structure Weight: 74.24 kDa 
  • Atom Count: 3,520 
  • Modeled Residue Count: 433 
  • Deposited Residue Count: 641 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone-lysine N-methyltransferase NSD2174Homo sapiensMutation(s): 0 
Gene Names: NSD2KIAA1090MMSETTRX5WHSC1
EC: 2.1.1.357
UniProt & NIH Common Fund Data Resources
Find proteins for O96028 (Homo sapiens)
Explore O96028 
Go to UniProtKB:  O96028
PHAROS:  O96028
GTEx:  ENSG00000109685 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO96028
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein cereblon467Homo sapiensMutation(s): 0 
Gene Names: CRBNAD-006
UniProt & NIH Common Fund Data Resources
Find proteins for Q96SW2 (Homo sapiens)
Explore Q96SW2 
Go to UniProtKB:  Q96SW2
PHAROS:  Q96SW2
GTEx:  ENSG00000113851 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96SW2
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1CSQ(
Subject of Investigation/LOI)

Query on A1CSQ



Download:Ideal Coordinates CCD File
C [auth A]1-(5-{9-[(4-{2-[(2S,3R)-2-(3,5-dichloro-4-fluorophenyl)-5-oxomorpholin-3-yl]ethyl}piperazin-1-yl)methyl]-3-azaspiro[5.5]undecane-3-carbonyl}-2-methylphenyl)-1,3-diazinane-2,4-dione
C39 H49 Cl2 F N6 O5
LDKYLKMCPUFNTL-PJTQZDKOSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
D [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other private--

Revision History  (Full details and data files)

  • Version 1.0: 2026-07-15
    Type: Initial release