9B7A | pdb_00009b7a

Crystal structure of peroxiredoxin 1 with RA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free: 
    0.192 (Depositor), 0.194 (DCC) 
  • R-Value Work: 
    0.165 (Depositor), 0.168 (DCC) 
  • R-Value Observed: 
    0.166 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


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Literature

Inhibited peroxidase activity of peroxiredoxin 1 by palmitic acid exacerbates nonalcoholic steatohepatitis in male mice.

Yin, W.Xu, H.Bai, Z.Wu, Y.Zhang, Y.Liu, R.Wang, Z.Zhang, B.Shen, J.Zhang, H.Chen, X.Ma, D.Shi, X.Yan, L.Zhang, C.Jiang, H.Chen, K.Guo, D.Niu, W.Yin, H.Zhang, W.J.Luo, C.Xie, X.

(2025) Nat Commun 16: 598-598

  • DOI: https://doi.org/10.1038/s41467-025-55939-2
  • Primary Citation Related Structures: 
    9B7A

  • PubMed Abstract: 

    Reactive oxygen species exacerbate nonalcoholic steatohepatitis (NASH) by oxidizing macromolecules; yet how they promote NASH remains poorly understood. Here, we show that peroxidase activity of global hepatic peroxiredoxin (PRDX) is significantly decreased in NASH, and palmitic acid (PA) binds to PRDX1 and inhibits its peroxidase activity. Using three genetic models, we demonstrate that hepatic PRDX1 protects against NASH in male mice. Mechanistically, PRDX1 suppresses STAT signaling and protects mitochondrial function by scavenging hydrogen peroxide, and mitigating the oxidation of protein tyrosine phosphatases and lipid peroxidation. We further identify rosmarinic acid (RA) as a potent agonist of PRDX1. As revealed by the complex crystal structure, RA binds to PRDX1 and stabilizes its peroxidatic cysteine. RA alleviates NASH through specifically activating PRDX1's peroxidase activity. Thus, beyond revealing the molecular mechanism underlying PA promoting oxidative stress and NASH, our study suggests that boosting PRDX1's peroxidase activity is a promising intervention for treating NASH.


  • Organizational Affiliation
    • NHC Key Laboratory of Hormones and Development, Tianjin Key Laboratory of Metabolic Diseases, The province and ministry co-sponsored collaborative innovation center for medical epigenetics, Chu Hsien-I Memorial Hospital & Tianjin Institute of Endocrinology, Tianjin Medical University, Tianjin, 300134, China.

Macromolecule Content 

  • Total Structure Weight: 39.03 kDa 
  • Atom Count: 3,042 
  • Modeled Residue Count: 336 
  • Deposited Residue Count: 350 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Peroxiredoxin-1
A, B
175Homo sapiensMutation(s): 0 
Gene Names: PRDX1PAGAPAGBTDPX2
EC: 1.11.1.24
UniProt & NIH Common Fund Data Resources
Find proteins for Q06830 (Homo sapiens)
Explore Q06830 
Go to UniProtKB:  Q06830
PHAROS:  Q06830
GTEx:  ENSG00000117450 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ06830
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ROA
(Subject of Investigation/LOI)

Query on ROA



Download:Ideal Coordinates CCD File
C [auth A](2R)-3-(3,4-dihydroxyphenyl)-2-{[(2E)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]oxy}propanoic acid
C18 H16 O8
DOUMFZQKYFQNTF-WUTVXBCWSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free:  0.192 (Depositor), 0.194 (DCC) 
  • R-Value Work:  0.165 (Depositor), 0.168 (DCC) 
  • R-Value Observed: 0.166 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.762α = 90
b = 78.573β = 90
c = 82.689γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China82104064

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-22
    Type: Initial release