9R11 | pdb_00009r11

Structure of the PRYSPRY domain of human MID2, crystal form II


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 
    0.206 (Depositor), 0.208 (DCC) 
  • R-Value Work: 
    0.155 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 
    0.158 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


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Literature

Structural analysis of TRIM family PRYSPRY domains and its implications for E3-ligand design.

Zhubi, R.Chaikuad, A.Munoz Sosa, C.J.Joerger, A.C.Knapp, S.

(2025) J Struct Biol X 12: 100134-100134

  • DOI: https://doi.org/10.1016/j.yjsbx.2025.100134
  • Primary Citation of Related Structures:  
    7B2S, 7QRY, 7QRZ, 7QS0, 7QS1, 7QS2, 7QS3, 7QS4, 7QS5, 9R11

  • PubMed Abstract: 

    Tripartite motif (TRIM) proteins constitute one of the largest subfamilies of RING-type E3 ubiquitin ligases and are attractive targets for the development of novel degraders that exploit the ubiquitin-proteasome pathway. More than half of all TRIM family members contain a PRYSPRY domain, a potentially druggable protein interaction module, located in their C-terminal region. Here, we have determined crystal structures of the PRYSPRY domains from nine TRIM family proteins: TRIM1 (MID2), TRIM9, TRIM10, TRIM11, TRIM15, TRIM16, TRIM18 (MID1), TRIM36, and TRIM67. These structures reveal conservation of the overall β-sandwich topology, despite low sequence conservation, with a unique subdomain swap observed in TRIM11. Significant variations were found in the loops flanking the canonical substrate-binding site, which modulate the shape and electrostatic properties of the binding pocket, hinting at substantial differences in substrate specificity and binding modes among family members. TRIM36 features a unique structural motif between the canonical β-strands 2 and 3, leading to the formation of a dimer, with the canonical substrate-binding site partially occluded by the dimerization motif. In addition, we mapped the locations of missense mutations in MID1 associated with X-linked Opitz syndrome, suggesting that some of these mutations impair the conformational stability of the protein. Taken together, our data provide intriguing insights into the structural and functional divergence of TRIM family PRYSPRY domains, their potential druggability and substrate recognition, and the challenges of ligand design.


  • Organizational Affiliation
    • Institute of Pharmaceutical Chemistry, Goethe University, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Probable E3 ubiquitin-protein ligase MID2A [auth B],
B [auth A]
190Homo sapiensMutation(s): 0 
Gene Names: MID2FXY2RNF60TRIM1
EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UJV3 (Homo sapiens)
Explore Q9UJV3 
Go to UniProtKB:  Q9UJV3
PHAROS:  Q9UJV3
GTEx:  ENSG00000080561 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UJV3
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free:  0.206 (Depositor), 0.208 (DCC) 
  • R-Value Work:  0.155 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 0.158 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.406α = 90
b = 60.919β = 90
c = 118.59γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European CommissionEuropean UnionEUbOPEN grant 875510

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-10
    Type: Initial release