8YOR | pdb_00008yor

Complex of HARSWHEP and a-HARSWHEP Fab


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.273 (Depositor), 0.273 (DCC) 
  • R-Value Work: 
    0.227 (Depositor), 0.228 (DCC) 
  • R-Value Observed: 
    0.229 (Depositor) 

Starting Models: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 8YOR

This is version 1.1 of the entry. See complete history

Literature

A human histidyl-tRNA synthetase splice variant therapeutic targets NRP2 to resolve lung inflammation and fibrosis.

Nangle, L.A.Xu, Z.Siefker, D.Burkart, C.Chong, Y.E.Zhai, L.Geng, Y.Polizzi, C.Guy, L.Eide, L.Tong, Y.Klopp-Savino, S.Ferrer, M.Rauch, K.Wang, A.Hamel, K.Crampton, S.Paz, S.Chiang, K.P.Do, M.H.Burman, L.Lee, D.Zhang, M.Ogilvie, K.King, D.Adams, R.A.Schimmel, P.

(2025) Sci Transl Med 17: eadp4754-eadp4754

  • DOI: https://doi.org/10.1126/scitranslmed.adp4754
  • Primary Citation Related Structures: 
    8YOR, 8YP1

  • PubMed Abstract: 

    Interstitial lung disease (ILD) consists of a group of immune-mediated disorders that can cause inflammation and progressive fibrosis of the lungs, representing an area of unmet medical need given the lack of disease-modifying therapies and toxicities associated with current treatment options. Tissue-specific splice variants (SVs) of human aminoacyl-tRNA synthetases (aaRSs) are catalytic nulls thought to confer regulatory functions. One example from human histidyl-tRNA synthetase (HARS), termed HARS WHEP because the splicing event resulted in a protein encompassing the WHEP-TRS domain of HARS (a structurally conserved domain found in multiple aaRSs), is enriched in human lung and up-regulated by inflammatory cytokines in lung and immune cells. Structural analysis of HARS WHEP confirmed a well-organized helix-turn-helix motif. This motif bound specifically and selectively to neuropilin-2 (NRP2), a receptor expressed by myeloid cells in active sites of inflammation, to inhibit expression of proinflammatory receptors and cytokines and to down-regulate inflammatory pathways in primary human macrophages. In animal models of lung injury and ILD, including bleomycin treatment, silicosis, sarcoidosis, chronic hypersensitivity pneumonitis, systemic sclerosis, and rheumatoid arthritis-ILD, HARS WHEP reduced lung inflammation, immune cell infiltration, and fibrosis. In patients with sarcoidosis, efzofitimod treatment resulted in down-regulation of gene expression for inflammatory pathways in peripheral immune cells and stabilization of inflammatory biomarkers in serum after steroid tapering. We demonstrate the immunomodulatory activity of HARS WHEP and present preclinical data supporting ongoing clinical development of the biologic efzofitimod based on HARS WHEP in ILD.


  • Organizational Affiliation
    • aTyr Pharma, San Diego, CA 92121, USA.

Macromolecule Content 

  • Total Structure Weight: 112.87 kDa 
  • Atom Count: 7,924 
  • Modeled Residue Count: 965 
  • Deposited Residue Count: 1,034 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
a-HARSWHEP Fab-light chainA,
D [auth C]
217Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
a-HARSWHEP Fab-heavy chainB,
F [auth D]
234Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Histidine--tRNA ligase, cytoplasmicC [auth E],
E [auth F]
66Homo sapiensMutation(s): 0 
Gene Names: HARS1HARSHRS
EC: 6.1.1.21
UniProt & NIH Common Fund Data Resources
Find proteins for P12081 (Homo sapiens)
Explore P12081 
Go to UniProtKB:  P12081
PHAROS:  P12081
GTEx:  ENSG00000170445 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12081
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.273 (Depositor), 0.273 (DCC) 
  • R-Value Work:  0.227 (Depositor), 0.228 (DCC) 
  • R-Value Observed: 0.229 (Depositor) 
Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.75α = 90
b = 113.56β = 106.6
c = 149.499γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data

  • Released Date: 2025-02-12 
  • Deposition Author(s): Zhai, L.

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-12
    Type: Initial release
  • Version 1.1: 2025-04-02
    Changes: Database references