6TDB

Neuropilin2-b1 domain in a complex with the C-terminal VEGFB167 peptide

Summary for 6TDB

• Entry DOI: 10.2210/pdb6tdb/pdb
• Descriptor: Neuropilin-2, C-terminal VEGFB167 peptide, 1,2-ETHANEDIOL, ... (5 entities in total)
• Functional Keywords: vegf-binding, nrp2, angiogenesis, immunomodulation, signaling protein
• Biological source: Homo sapiens (Human); More
• Total number of polymer chains: 7
• Total formula weight: 75900.39

Authors

Eldrid, C.,Yu, L.,Yelland, T.,Fotinou, C.,Djordjevic, S. (deposition date: 2019-11-08, release date: 2020-11-18, Last modification date: 2026-03-25)

Primary citation

Eldrid, C.,Zloh, M.,Fotinou, C.,Yelland, T.,Yu, L.,Mota, F.,Selwood, D.L.,Djordjevic, S.
VEGFA, B, C: Implications of the C-Terminal Sequence Variations for the Interaction with Neuropilins.
Biomolecules, 12:-, 2022

PubMed Abstract: Vascular endothelial growth factors (VEGFs) are the key regulators of blood and lymphatic vessels' formation and function. Each of the proteins from the homologous family VEGFA, VEGFB, VEGFC and VEGFD employs a core cysteine-knot structural domain for the specific interaction with one or more of the cognate tyrosine kinase receptors. Additional diversity is exhibited by the involvement of neuropilins-transmembrane co-receptors, whose b1 domain contains the binding site for the C-terminal sequence of VEGFs. Although all relevant isoforms of VEGFs that interact with neuropilins contain the required C-terminal Arg residue, there is selectivity of neuropilins and VEGF receptors for the VEGF proteins, which is reflected in the physiological roles that they mediate. To decipher the contribution made by the C-terminal sequences of the individual VEGF proteins to that functional differentiation, we determined structures of molecular complexes of neuropilins and VEGF-derived peptides and examined binding interactions for all neuropilin-VEGF pairs experimentally and computationally. While X-ray crystal structures and ligand-binding experiments highlighted similarities between the ligands, the molecular dynamics simulations uncovered conformational preferences of VEGF-derived peptides beyond the C-terminal arginine that contribute to the ligand selectivity of neuropilins. The implications for the design of the selective antagonists of neuropilins' functions are discussed.

PubMed: 35327564
DOI: 10.3390/biom12030372

Experimental method

X-RAY DIFFRACTION (2.45 Å)