4ZYA

The N-terminal extension domain of human asparaginyl-tRNA synthetase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.210 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Unique N-terminal extension domain of human asparaginyl-tRNA synthetase elicits CCR3-mediated chemokine activity.

Park, J.S.Park, M.C.Lee, K.Y.Goughnour, P.C.Jeong, S.J.Kim, H.S.Kim, H.J.Lee, B.J.Kim, S.Han, B.W.

(2018) Int J Biol Macromol 120: 835-845

  • DOI: https://doi.org/10.1016/j.ijbiomac.2018.08.171
  • Primary Citation of Related Structures:  
    4ZYA, 5XIX

  • PubMed Abstract: 

    Asparaginyl-tRNA synthetase (NRS) is not only essential in protein translation but also associated with autoimmune diseases. Particularly, patients with antibodies that recognize NRS often develop interstitial lung disease (ILD). However, the underlying mechanism of how NRS is recognized by immune cells and provokes inflammatory responses is not well-understood. Here, we found that the crystal structure of the unique N-terminal extension domain of human NRS (named as UNE-N, where -N denotes NRS) resembles that of the chemotactic N-terminal domain of NRS from a filarial nematode, Brugia malayi, which recruits and activates specific immune cells by interacting with CXC chemokine receptor 1 and 2. UNE-N induced migration of CC chemokine receptor 3 (CCR3)-expressing cells. The chemokine activity of UNE-N was significantly reduced by suppressing CCR3 expression with CCR3-targeting siRNA, and the loop3 region of UNE-N was shown to interact mainly with the extracellular domains of CCR3 in nuclear magnetic resonance perturbation experiments. Based on these results, evolutionarily acquired UNE-N elicits chemokine activities that would promote NRS-CCR3-mediated proinflammatory signaling in ILD.


  • Organizational Affiliation

    Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Asparagine--tRNA ligase, cytoplasmic
A, B
77Homo sapiensMutation(s): 0 
Gene Names: NARS
EC: 6.1.1.22
UniProt & NIH Common Fund Data Resources
Find proteins for O43776 (Homo sapiens)
Explore O43776 
Go to UniProtKB:  O43776
PHAROS:  O43776
GTEx:  ENSG00000134440 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO43776
Sequence Annotations
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.210 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 32.626α = 90
b = 32.626β = 90
c = 215.921γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science, ICT and Future Planning of KoreaKorea, Republic Of2013M3A6A4043695

Revision History  (Full details and data files)

  • Version 1.0: 2016-05-25
    Type: Initial release
  • Version 1.1: 2019-04-24
    Changes: Data collection, Database references, Derived calculations
  • Version 1.2: 2024-10-16
    Changes: Data collection, Database references, Derived calculations, Structure summary