8GV3 | pdb_00008gv3

The cryo-EM structure of GSNOR with NYY001


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.05 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

S -nitrosoglutathione reductase as a therapeutic target for diabetic vascular complications in rodent models.

Zhao, S.Song, T.Tang, X.Fan, C.Yang, Y.Zhang, Z.Xia, Y.Zhang, Y.Cao, J.Wang, Z.Shi, Z.Tang, X.Wang, D.Yin, G.Zhang, S.Gao, Y.Chen, H.Wang, L.Chen, F.Wang, H.Yu, B.Cao, Y.Sun, K.Liu, X.Wang, X.Yan, C.Han, Y.Han, Y.Xie, L.Ji, Y.

(2025) Sci Transl Med 17: eadn9216-eadn9216

  • DOI: https://doi.org/10.1126/scitranslmed.adn9216
  • Primary Citation of Related Structures:  
    8GV3

  • PubMed Abstract: 

    Endothelial dysfunction is one of the earliest processes in diabetes and a major contributor to diabetic vascular complications, which often exhibit limited response to glucose-lowering therapies. We identified up-regulated S -nitrosoglutathione reductase (GSNOR) as a critical factor associated with diabetic vascular complications by unbiased proteomics. Elevated GSNOR expression was observed in the endothelium of patients with type 2 diabetes and in streptozotocin (STZ)-induced type 1 diabetes mice as well as in db/db type 2 diabetes mouse models. Genetic ablation of endothelial Gsnor promoted angiogenesis, maintained vascular permeability, and improved vasodilation in type 1 diabetes mice induced by STZ. GSNOR deficiency protected against high glucose-induced endothelial dysfunction in vitro, as evidenced by rescued tube formation, enhanced spheroid sprouting, maintained barrier integrity, and reduced permeability. Mechanistically, GSNOR orchestrated endothelial dysfunction independently of its enzymatic activity by binding the transcription factor ETS-related gene (ERG) and triggered its nuclear export through chromosome region maintenance 1. We synthesized NYY-001, an oral agent, that selectively blocks the GSNOR-ERG interaction. The direct targeting of NYY-001 to GSNOR was determined by resolving the crystal structure of their complex using cryo-electron microscopy. NYY-001 treatment enhanced postischemic neovascularization and restored vascular permeability in the peripheral vasculature in STZ-induced type 1 diabetes and db/db type 2 diabetes mouse models. These findings reveal a mechanistic role for the GSNOR-ERG complex in diabetic vascular complications and highlight NYY-001 as a promising therapeutic candidate.


  • Organizational Affiliation
    • Key Laboratory of Drug Targets and Translational Medicine for Cardio-cerebrovascular Diseases; Medical Basic Research Innovation Center for Cardiovascular and Cerebrovascular Diseases, Ministry of Education; Key Laboratory of Targeted Intervention of Cardiovascular Disease; Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Nanjing Medical University, Nanjing 211166, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Alcohol dehydrogenase class-3
A, B
375Homo sapiensMutation(s): 0 
Gene Names: ADH5ADHXFDH
EC: 1.1.1.1 (PDB Primary Data), 1.1.1 (PDB Primary Data), 1.1.1.284 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P11766 (Homo sapiens)
Explore P11766 
Go to UniProtKB:  P11766
PHAROS:  P11766
GTEx:  ENSG00000197894 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11766
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B]
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
WKZ (Subject of Investigation/LOI)
Query on WKZ

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B]
(4P)-4-{2-[4-(1H-imidazol-1-yl)phenyl]-5-[3-oxo-3-(2-oxo-1,3-thiazolidin-3-yl)propyl]-1H-pyrrol-1-yl}-3-methylbenzamide
C27 H25 N5 O3 S
RXCKIKOJUHFVSP-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
G [auth B],
H [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.05 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China2018YFC1004704
National Natural Science Foundation of China (NSFC)China82072468

Revision History  (Full details and data files)

  • Version 1.0: 2023-09-20
    Type: Initial release
  • Version 1.1: 2025-06-04
    Changes: Data collection, Structure summary
  • Version 1.2: 2025-10-08
    Changes: Data collection, Database references