9DRY | pdb_00009dry

CHIP U-box dimer bound to Fab 2F1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.02 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

Recombinant antibodies inhibit enzymatic activity of the E3 ubiquitin ligase CHIP via multiple mechanisms.

Chung, D.H.Connelly, E.J.Unnikrishnan, A.Chuo, S.W.Wucherer, K.Nadel, C.M.Gestwicki, J.E.Southworth, D.R.Craik, C.S.

(2025) J Biological Chem 301: 108220-108220

  • DOI: https://doi.org/10.1016/j.jbc.2025.108220
  • Primary Citation of Related Structures:  
    9DRY

  • PubMed Abstract: 

    Carboxyl-terminus of Hsp70-Interacting Protein (CHIP) is an E3 ubiquitin ligase that marks misfolded substrates for degradation. Hyper-activation of CHIP has been implicated in multiple diseases, including cystic fibrosis and cancer, suggesting that it may be a potential drug target. However, there are few tools available for exploring this possibility. Moreover, the best ways of inhibiting CHIP's function are not obvious, as this complex protein is composed of a tetratricopeptide repeat (TPR) domain, a U-box domain, and a coiled-coil domain that mediates homodimerization. To probe the structure and function of CHIP, we report an antibody panning campaign that yielded six recombinant Fabs with affinity for CHIP. Interestingly, these antibodies varied in their binding site(s) and impact on CHIP function, such as inhibiting TPR interactions, autoubiquitination, and/or substrate ubiquitination. Of particular interest, antibody 2F1 nearly eliminated substrate binding (IC 50  = 2.7 μM) and limited ubiquitination and autoubiquitination. Cryo-electron microscopy of the 2F1:CHIP complex revealed a 2:1 binding mode (Fab:CHIP dimer), with 2F1 bound to the U-box domain and simultaneously displacing the TPR domain. Together, these studies provide insight into ways of inhibiting CHIP's activity and provide a series of new probes for exploring the function of this important E3 ubiquitin ligase.


  • Organizational Affiliation
    • Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA. Electronic address: dhnc86@gmail.com.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase CHIPA,
D [auth B]
75Homo sapiensMutation(s): 0 
Gene Names: STUB1CHIPPP1131
EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UNE7 (Homo sapiens)
Explore Q9UNE7 
Go to UniProtKB:  Q9UNE7
PHAROS:  Q9UNE7
GTEx:  ENSG00000103266 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UNE7
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
2F1 Fab heavy chainB [auth E],
E [auth G]
222Homo sapiensMutation(s): 0 
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Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
2F1 Fab light chainC [auth F],
F [auth H]
215Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.02 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
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Revision History  (Full details and data files)

  • Version 1.0: 2025-03-12
    Type: Initial release