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PDBsum entry 5dn2
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Signaling protein
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PDB id
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5dn2
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PDB id:
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| Name: |
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Signaling protein
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Title:
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Human nrp2 b1 domain in complex with the peptide corresponding to the c-terminus of vegf-a
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Structure:
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Neuropilin-2. Chain: a, b, c, d. Fragment: neuropilin-2 domain b1 f5/8 typE C 1, unp residues 275-429. Synonym: vascular endothelial cell growth factor 165 receptor 2. Engineered: yes. Vascular endothelial growth factor a. Chain: f, g, e. Fragment: vegf-a165-hbd, unp residues 205-232. Synonym: vegf-a,vascular permeability factor,vpf.
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Source:
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Homo sapiens. Human. Organism_taxid: 9606. Gene: nrp2, vegf165r2. Expressed in: escherichia coli. Expression_system_taxid: 83333. Expression_system_variant: rosetta-gami 2(de3)plyss. Gene: vegfa, vegf. Expression_system_variant: shuffle.
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Resolution:
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1.95Å
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R-factor:
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0.206
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R-free:
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0.234
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Authors:
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Y.C.I.Tsai,P.Frankel,C.Fotinou,R.Rana,I.Zachary,S.Djordjevic
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Key ref:
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Y.C.Tsai
et al.
(2016).
Structural studies of neuropilin-2 reveal a zinc ion binding site remote from the vascular endothelial growth factor binding pocket.
Febs J,
283,
1921-1934.
PubMed id:
DOI:
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Date:
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09-Sep-15
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Release date:
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20-Jul-16
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PROCHECK
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Headers
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References
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O60462
(NRP2_HUMAN) -
Neuropilin-2 from Homo sapiens
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Seq:
Struc:
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931 a.a.
156 a.a.*
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Key: |
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PfamA domain |
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Secondary structure |
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CATH domain |
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*
PDB and UniProt seqs differ
at 1 residue position (black
cross)
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DOI no:
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Febs J
283:1921-1934
(2016)
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PubMed id:
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Structural studies of neuropilin-2 reveal a zinc ion binding site remote from the vascular endothelial growth factor binding pocket.
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Y.C.Tsai,
C.Fotinou,
R.Rana,
T.Yelland,
P.Frankel,
I.Zachary,
S.Djordjevic.
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ABSTRACT
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Neuropilin-2 is a transmembrane receptor involved in lymphangiogenesis and
neuronal development. In adults, neuropilin-2 and its homologous protein
neuropilin-1 have been implicated in cancers and infection. Molecular
determinants of the ligand selectivity of neuropilins are poorly understood. We
have identified and structurally characterized a zinc ion binding site on human
neuropilin-2. The neuropilin-2-specific zinc ion binding site is located near
the interface between domains b1 and b2 in the ectopic region of the protein,
remote from the neuropilin binding site for its physiological ligand, i.e.
vascular endothelial growth factor. We also present an X-ray crystal structure
of the neuropilin-2 b1 domain in a complex with the C-terminal sub-domain of
VEGF-A. Zn(2+) binding to neuropilin-2 destabilizes the protein structure but
this effect was counteracted by heparin, suggesting that modifications by
glycans and zinc in the extracellular matrix may affect functional neuropilin-2
ligand binding and signalling activity.
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Links
