8YHU | pdb_00008yhu

hTLR3/minibinder 8.6


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.88 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

De novo design of protein minibinder agonists of TLR3.

Adams, C.S.Kim, H.Burtner, A.E.Lee, D.S.Dobbins, C.Criswell, C.Coventry, B.Tran-Pearson, A.Kim, H.M.King, N.P.

(2025) Nat Commun 16: 1234-1234

  • DOI: https://doi.org/10.1038/s41467-025-56369-w
  • Primary Citation Related Structures: 
    8YHT, 8YHU

  • PubMed Abstract: 

    Toll-like Receptor 3 (TLR3) is a pattern recognition receptor that initiates antiviral immune responses upon binding double-stranded RNA (dsRNA). Several nucleic acid-based TLR3 agonists have been explored clinically as vaccine adjuvants in cancer and infectious disease, but present substantial manufacturing and formulation challenges. Here, we use computational protein design to create novel miniproteins that bind to human TLR3 with nanomolar affinities. Cryo-EM structures of two minibinders in complex with TLR3 reveal that they bind the target as designed, although one partially unfolds due to steric competition with a nearby N-linked glycan. Multivalent forms of both minibinders induce NF-κB signaling in TLR3-expressing cell lines, demonstrating that they may have therapeutically relevant biological activity. Our work provides a foundation for the development of specific, stable, and easy-to-formulate protein-based agonists of TLRs and other pattern recognition receptors.


  • Organizational Affiliation
    • Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA.

Macromolecule Content 

  • Total Structure Weight: 86.42 kDa 
  • Atom Count: 5,990 
  • Modeled Residue Count: 719 
  • Deposited Residue Count: 730 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Toll-like receptor 3674Homo sapiensMutation(s): 0 
Gene Names: TLR3
UniProt & NIH Common Fund Data Resources
Find proteins for O15455 (Homo sapiens)
Explore O15455 
Go to UniProtKB:  O15455
PHAROS:  O15455
GTEx:  ENSG00000164342 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO15455
Glycosylation
Glycosylation Sites: 10Go to GlyGen: O15455-1
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
minibinder 8.656Homo sapiensMutation(s): 0 

Oligosaccharides

Help  
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C, D, E, F, G
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.88 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
Other government--

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-05
    Type: Initial release
  • Version 1.1: 2025-06-04
    Changes: Data collection, Database references
  • Version 1.2: 2025-07-02
    Changes: Data collection