7P5U | pdb_00007p5u

Neuropilin-b1 in a complex with a VEGFB-derived peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 
    0.214 (Depositor), 0.221 (DCC) 
  • R-Value Work: 
    0.188 (Depositor), 0.199 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7P5U

This is version 1.3 of the entry. See complete history

Literature

Peptides Derived from Vascular Endothelial Growth Factor B Show Potent Binding to Neuropilin-1.

Mota, F.Yelland, T.Hutton, J.A.Parker, J.Patsiarika, A.Chan, A.W.E.O'Leary, A.Fotinou, C.Martin, J.F.Zachary, I.C.Djordjevic, S.Frankel, P.Selwood, D.L.

(2022) Chembiochem 23: e202100463-e202100463

  • DOI: https://doi.org/10.1002/cbic.202100463
  • Primary Citation Related Structures: 
    7P5U

  • PubMed Abstract: 

    Vascular endothelial growth factors (VEGFs) regulate significant pathways in angiogenesis, myocardial and neuronal protection, metabolism, and cancer progression. The VEGF-B growth factor is involved in cell survival, anti-apoptotic and antioxidant mechanisms, through binding to VEGF receptor 1 and neuropilin-1 (NRP1). We employed surface plasmon resonance technology and X-ray crystallography to analyse the molecular basis of the interaction between VEGF-B and the b1 domain of NRP1, and developed VEGF-B C-terminus derived peptides to be used as chemical tools for studying VEGF-B - NRP1 related pathways. Peptide lipidation was used as a means to stabilise the peptides. VEGF-B-derived peptides containing a C-terminal arginine show potent binding to NRP1-b1. Peptide lipidation increased binding residence time and improved plasma stability. A crystal structure of a peptide with NRP1 demonstrated that VEGF-B peptides bind at the canonical C-terminal arginine binding site. VEGF-B C-terminus imparts higher affinity for NRP1 than the corresponding VEGF-A 165 region. This tight binding may impact on the activity and selectivity of the full-length protein. The VEGF-B 167 derived peptides were more effective than VEGF-A 165 peptides in blocking functional phosphorylation events. Blockers of VEGF-B function have potential applications in diabetes and non-alcoholic fatty liver disease.


  • Organizational Affiliation
    • Wolfson Institute for Biomedical Research, University College London, Gower Street, London, WC1E 6BT, UK.

Macromolecule Content 

  • Total Structure Weight: 38.92 kDa 
  • Atom Count: 2,772 
  • Modeled Residue Count: 317 
  • Deposited Residue Count: 342 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Neuropilin-1A [auth AAA],
B [auth BBB]
158Homo 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
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
MGC0122C [auth CCC],
D [auth EEE]
13Homo sapiensMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free:  0.214 (Depositor), 0.221 (DCC) 
  • R-Value Work:  0.188 (Depositor), 0.199 (DCC) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.496α = 90
b = 74.35β = 90
c = 91.426γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
British Heart FoundationUnited KingdomPG/10/52/28448

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-27
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-11-06
    Changes: Structure summary
  • Version 1.3: 2026-03-25
    Changes: Database references