7UIH

PSMD2 Structure


Experimental Data Snapshot

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

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

Targeted degradation via direct 26S proteasome recruitment.

Bashore, C.Prakash, S.Johnson, M.C.Conrad, R.J.Kekessie, I.A.Scales, S.J.Ishisoko, N.Kleinheinz, T.Liu, P.S.Popovych, N.Wecksler, A.T.Zhou, L.Tam, C.Zilberleyb, I.Srinivasan, R.Blake, R.A.Song, A.Staben, S.T.Zhang, Y.Arnott, D.Fairbrother, W.J.Foster, S.A.Wertz, I.E.Ciferri, C.Dueber, E.C.

(2023) Nat Chem Biol 19: 55-63

  • DOI: https://doi.org/10.1038/s41589-022-01218-w
  • Primary Citation of Related Structures:  
    7UIH, 7UJD

  • PubMed Abstract: 

    Engineered destruction of target proteins by recruitment to the cell's degradation machinery has emerged as a promising strategy in drug discovery. The majority of molecules that facilitate targeted degradation do so via a select number of ubiquitin ligases, restricting this therapeutic approach to tissue types that express the requisite ligase. Here, we describe a new strategy of targeted protein degradation through direct substrate recruitment to the 26S proteasome. The proteolytic complex is essential and abundantly expressed in all cells; however, proteasomal ligands remain scarce. We identify potent peptidic macrocycles that bind directly to the 26S proteasome subunit PSMD2, with a 2.5-Å-resolution cryo-electron microscopy complex structure revealing a binding site near the 26S pore. Conjugation of this macrocycle to a potent BRD4 ligand enabled generation of chimeric molecules that effectively degrade BRD4 in cells, thus demonstrating that degradation via direct proteasomal recruitment is a viable strategy for targeted protein degradation.


  • Organizational Affiliation

    Department of Early Discovery Biochemistry, Genentech Inc., South San Francisco, CA, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 2644Homo sapiensMutation(s): 0 
Gene Names: PSMD2TRAP2
UniProt & NIH Common Fund Data Resources
Find proteins for Q13200 (Homo sapiens)
Explore Q13200 
Go to UniProtKB:  Q13200
PHAROS:  Q13200
GTEx:  ENSG00000175166 
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UniProt GroupQ13200
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fab 14 LC CDRsB [auth C]217Homo sapiensMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Fab 14 HC CDRsC [auth D]231Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Fab 8 LC CDRsD [auth E]217Homo sapiensMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Fab 8 HC CDRsE [auth F]229Homo sapiensMutation(s): 0 
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  • Reference Sequence
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

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-01-11
    Type: Initial release
  • Version 1.1: 2024-06-12
    Changes: Data collection, Refinement description