structure of PTP-MEG2 and NSF-pY83 peptide complex

Experimental Data Snapshot

  • Resolution: 1.70 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.185 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


PTP-MEG2 regulates quantal size and fusion pore opening through two distinct structural bases and substrates.

Xu, Y.F.Chen, X.Yang, Z.Xiao, P.Liu, C.H.Li, K.S.Yang, X.Z.Wang, Y.J.Zhu, Z.L.Xu, Z.G.Zhang, S.Wang, C.Song, Y.C.Zhao, W.D.Wang, C.H.Ji, Z.L.Zhang, Z.Y.Cui, M.Sun, J.P.Yu, X.

(2021) EMBO Rep 22: e52141-e52141

  • DOI: https://doi.org/10.15252/embr.202052141
  • Primary Citation of Related Structures:  
    6KZQ, 6L03

  • PubMed Abstract: 

    Tyrosine phosphorylation of secretion machinery proteins is a crucial regulatory mechanism for exocytosis. However, the participation of protein tyrosine phosphatases (PTPs) in different exocytosis stages has not been defined. Here we demonstrate that PTP-MEG2 controls multiple steps of catecholamine secretion. Biochemical and crystallographic analyses reveal key residues that govern the interaction between PTP-MEG2 and its substrate, a peptide containing the phosphorylated NSF-pY 83 site, specify PTP-MEG2 substrate selectivity, and modulate the fusion of catecholamine-containing vesicles. Unexpectedly, delineation of PTP-MEG2 mutants along with the NSF binding interface reveals that PTP-MEG2 controls the fusion pore opening through NSF independent mechanisms. Utilizing bioinformatics search and biochemical and electrochemical screening approaches, we uncover that PTP-MEG2 regulates the opening and extension of the fusion pore by dephosphorylating the DYNAMIN2-pY 125 and MUNC18-1-pY 145 sites. Further structural and biochemical analyses confirmed the interaction of PTP-MEG2 with MUNC18-1-pY 145 or DYNAMIN2-pY 125 through a distinct structural basis compared with that of the NSF-pY 83 site. Our studies thus provide mechanistic insights in complex exocytosis processes.

  • Organizational Affiliation

    Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, Shandong University School of Medicine, Jinan, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine-protein phosphatase non-receptor type 9307Homo sapiensMutation(s): 0 
Gene Names: PTPN9
UniProt & NIH Common Fund Data Resources
Find proteins for P43378 (Homo sapiens)
Explore P43378 
Go to UniProtKB:  P43378
PHAROS:  P43378
GTEx:  ENSG00000169410 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP43378
Sequence Annotations
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NSF-pY83 peptideB [auth F]9Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P46459 (Homo sapiens)
Explore P46459 
Go to UniProtKB:  P46459
PHAROS:  P46459
GTEx:  ENSG00000073969 
Entity Groups  
UniProt GroupP46459
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on PTR
Experimental Data & Validation

Experimental Data

  • Resolution: 1.70 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.185 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.447α = 90
b = 83.708β = 90
c = 48.615γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-30
    Type: Initial release
  • Version 1.1: 2021-10-13
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Refinement description