8OV6

Ternary structure of intramolecular bivalent glue degrader IBG1 bound to BRD4 and DCAF16:DDB1deltaBPB


Experimental Data Snapshot

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

Starting Models: experimental, other
View more details

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Targeted protein degradation via intramolecular bivalent glues.

Hsia, O.Hinterndorfer, M.Cowan, A.D.Iso, K.Ishida, T.Sundaramoorthy, R.Nakasone, M.A.Imrichova, H.Schatz, C.Rukavina, A.Husnjak, K.Wegner, M.Correa-Saez, A.Craigon, C.Casement, R.Maniaci, C.Testa, A.Kaulich, M.Dikic, I.Winter, G.E.Ciulli, A.

(2024) Nature 627: 204-211

  • DOI: https://doi.org/10.1038/s41586-024-07089-6
  • Primary Citation of Related Structures:  
    8OV6

  • PubMed Abstract: 

    Targeted protein degradation is a pharmacological modality that is based on the induced proximity of an E3 ubiquitin ligase and a target protein to promote target ubiquitination and proteasomal degradation. This has been achieved either via proteolysis-targeting chimeras (PROTACs)-bifunctional compounds composed of two separate moieties that individually bind the target and E3 ligase, or via molecular glues that monovalently bind either the ligase or the target 1-4 . Here, using orthogonal genetic screening, biophysical characterization and structural reconstitution, we investigate the mechanism of action of bifunctional degraders of BRD2 and BRD4, termed intramolecular bivalent glues (IBGs), and find that instead of connecting target and ligase in trans as PROTACs do, they simultaneously engage and connect two adjacent domains of the target protein in cis. This conformational change 'glues' BRD4 to the E3 ligases DCAF11 or DCAF16, leveraging intrinsic target-ligase affinities that do not translate to BRD4 degradation in the absence of compound. Structural insights into the ternary BRD4-IBG1-DCAF16 complex guided the rational design of improved degraders of low picomolar potency. We thus introduce a new modality in targeted protein degradation, which works by bridging protein domains in cis to enhance surface complementarity with E3 ligases for productive ubiquitination and degradation.


  • Organizational Affiliation

    Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DDB1deltaBPB836Homo sapiensMutation(s): 0 
Gene Names: DDB1
UniProt & NIH Common Fund Data Resources
Find proteins for Q16531 (Homo sapiens)
Explore Q16531 
Go to UniProtKB:  Q16531
PHAROS:  Q16531
GTEx:  ENSG00000167986 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16531
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DDB1- and CUL4-associated factor 16218Homo sapiensMutation(s): 0 
Gene Names: DCAF16C4orf30
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NXF7 (Homo sapiens)
Explore Q9NXF7 
Go to UniProtKB:  Q9NXF7
PHAROS:  Q9NXF7
GTEx:  ENSG00000163257 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NXF7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Bromodomain-containing protein 4419Homo sapiensMutation(s): 0 
Gene Names: BRD4HUNK1
UniProt & NIH Common Fund Data Resources
Find proteins for O60885 (Homo sapiens)
Explore O60885 
Go to UniProtKB:  O60885
PHAROS:  O60885
GTEx:  ENSG00000141867 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60885
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
U79
Query on U79

Download Ideal Coordinates CCD File 
E [auth C]methyl 2-[(9~{S})-7-[4-[4-[[4-[(3-cyano-4-methyl-1~{H}-indol-7-yl)sulfamoyl]phenyl]methylcarbamoyl]phenyl]phenyl]-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoate
C44 H38 N8 O5 S2
HHSZFSOLNUHGMP-BHVANESWSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
D [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
U79 BindingDB:  8OV6 IC50: 29 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.77 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC
MODEL REFINEMENTPHENIX1.20.1-4487
MODEL REFINEMENTUCSF ChimeraX1.6.dev202302040126
MODEL REFINEMENTISOLDE1.6.dev1

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
H2020 Marie Curie Actions of the European CommissionEuropean Union101024945
European Research Council (ERC)European UnionERC-2012-StG-311460
Innovative Medicines InitiativeSwitzerland875510
Wellcome TrustUnited Kingdom223816/Z/21/Z
Medical Research Council (MRC, United Kingdom)United Kingdom4050845509
European Research Council (ERC)European Union851478
Austrian Science FundAustriaP32125
Austrian Science FundAustriaP31690
Austrian Science FundAustriaP7909

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-17
    Type: Initial release
  • Version 1.1: 2023-08-16
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-10
    Changes: Database references, Refinement description, Structure summary
  • Version 1.3: 2024-02-21
    Changes: Database references
  • Version 1.4: 2024-03-06
    Changes: Database references
  • Version 1.5: 2024-03-13
    Changes: Database references