9EOU

Crystal Structure of the b1b2 domains from Human Neuropilin-1 in complex with a peptide.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Identification of an osteopontin-derived peptide that binds neuropilin-1 and activates vascular repair responses and angiogenesis.

Chen, Y.Gialeli, C.Shen, J.Duner, P.Walse, B.Duelli, A.Caing-Carlsson, R.Blom, A.M.Zibert, J.R.Nilsson, A.H.Alenfall, J.Liang, C.Nilsson, J.

(2024) Pharmacol Res 205: 107259-107259

  • DOI: https://doi.org/10.1016/j.phrs.2024.107259
  • Primary Citation of Related Structures:  
    9EOU

  • PubMed Abstract: 

    The osteopontin-derived peptide FOL-005 stimulates hair growth. Using ligand-receptor glyco-capture technology we identified neuropilin-1 (NRP-1), a known co-receptor for vascular endothelial growth factor (VEGF) receptors, as the most probable receptor for FOL-005 and the more stable analogue FOL-026. X-ray diffraction and microscale thermophoresis analysis revealed that FOL-026 shares binding site with VEGF in the NRP-1 b1-subdomain. Stimulation of human umbilical vein endothelial cells with FOL-026 resulted in phosphorylation of VEGFR-2, ERK1/2 and AKT, increased cell growth and migration, stimulation of endothelial tube formation and inhibition of apoptosis in vitro. FOL-026 also promoted angiogenesis in vivo as assessed by subcutaneous Matrigel plug and hind limb ischemia models. NRP-1 knock-down or treatment of NRP-1 antagonist EG00229 blocked the stimulatory effects of FOL-026 on endothelial cells. Exposure of human coronary artery smooth muscle cells to FOL-026 stimulated cell growth, migration, inhibited apoptosis, and induced VEGF gene expression and VEGFR-2/AKT phosphorylation by an NRP-1-dependent mechanism. RNA sequencing showed that FOL-026 activated pathways involved in tissue repair. These findings identify NRP-1 as the receptor for FOL-026 and show that its biological effects mimic that of growth factors binding to the VEGF receptor family. They also suggest that FOL-026 may have therapeutical potential in conditions that require vascular repair and/or enhanced angiogenesis.


  • Organizational Affiliation

    Department of Cardiology, Second Affiliated Hospital of Naval Medical University, Shanghai Cardiovascular Institute of Integrative Medicine, Shanghai, China; Department of Experimental Medical Science, Lund University, Sweden.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Neuropilin-1318Homo sapiensMutation(s): 0 
Gene Names: NRP1NRPVEGF165R
UniProt & NIH Common Fund Data Resources
Find proteins for O14786 (Homo sapiens)
Explore O14786 
Go to UniProtKB:  O14786
PHAROS:  O14786
GTEx:  ENSG00000099250 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO14786
Sequence Annotations
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
OsteopontinB [auth P]15Homo sapiensMutation(s): 1 
UniProt & NIH Common Fund Data Resources
Find proteins for P10451 (Homo sapiens)
Explore P10451 
Go to UniProtKB:  P10451
PHAROS:  P10451
GTEx:  ENSG00000118785 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10451
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.69α = 90
b = 34.91β = 102.2
c = 69.97γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Novo Nordisk FoundationDenmark--
Swedish Research CouncilSweden--
VinnovaSweden--

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-26
    Type: Initial release