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 21AA | pdb_000021aa

Structure of Human Aspartate--tRNA ligase 3-154 with linker and FC : ATYR0101


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.96 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Validation slider image for 21AA

This is version 1.0 of the entry. See complete history. 

Literature

Natural Asp-tRNA Synthetase Fragment Targets Myofibroblasts to Abrogate Tissue Fibrosis.

Adams, R.A., Wang, Y.T., Barber, A.G., Hamel, K., Imfeld, A., Burman, L., Rauch, K., Chong, Y.E., Villanueva, A., Guy, L., Liu, W., Manzo, C., Klopp-Savino, S., Polizzi, C., Stamps, J., Pastenes, M., Tian, H., Fung, C.P., Zhang, Y., Hugo Ho, K.W., Sangiorgi, B., Dillingham, B., Brust, T.F., Chiang, K.P., Wu, Z., Xu, Z., Burkart, C., Nangle, L.A.

(2026) J Biol Chem : 113586-113586

  • DOI: https://doi.org/10.1016/j.jbc.2026.113586
  • Primary Citation Related Structures: 
    21AA

  • PubMed Abstract: 

    Fibrosis remains a major global health challenge with limited therapies that only slow disease progression. While the aminoacyl-tRNA synthetase (aaRS) family is known to utilize evolutionarily appended domains as extracellular signaling molecules, their role in regulating the homeostasis of the fibrotic process is poorly defined. We identify a natural proteolytic fragment of aspartyl-tRNA synthetase (DARS), termed DARS-N1, that selectively triggers apoptosis in myofibroblasts by targeting latent-transforming growth factor beta binding protein 1 (LTBP-1) on the extracellular matrix (ECM). This active N-terminal fragment of DARS reduces focal adhesion kinase (FAK) activation in undifferentiated fibroblasts and myofibroblasts, while only myofibroblasts exhibit inadequate cell-matrix attachment leading to loss of anchorage-dependent survival and promotion of apoptosis. We utilized ATYR0101, a therapeutic form of DARS-N1 engineered for extended serum exposure, to demonstrate anti-fibrotic activity in lung (bleomycin). Spatial transcriptomics analysis showed that ATYR0101 activates a restorative program promoting the return to a healthy state. These findings highlight ATYR0101's potential as a transformative therapy for disrupting the process of chronic tissue fibrosis.


  • Organizational Affiliation: 
    • aTyr Pharma, San Diego, CA, USA.

Macromolecule Content 

  • Total Structure Weight: 91.06 kDa 
  • Atom Count: 6,124 
  • Modeled Residue Count: 788 
  • Deposited Residue Count: 824 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Aspartate--tRNA ligase, cytoplasmic,linker+FC
A, B
412Homo sapiensMutation(s): 3 
Gene Names: DARS1, DARS, PIG40
EC: 6.1.1.12
UniProt & NIH Common Fund Data Resources
Find proteins for P14868 (Homo sapiens)
Explore P14868 
Go to UniProtKB:  P14868
PHAROS:  P14868
GTEx:  ENSG00000115866 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14868
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.96 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX"2.0_5885"
RECONSTRUCTIONcryoSPARC4.7.0

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentHong Kong--

Revision History  (Full details and data files)

  • Version 1.0: 2026-10-14
    Type: Initial release