5DN2 | pdb_00005dn2

Human NRP2 b1 domain in complex with the peptide corresponding to the C-terminus of VEGF-A

PDB DOI: https://doi.org/10.2210/pdb5DN2/pdb

Classification: SIGNALING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli K-12
Mutation(s): No

Deposited: 2015-09-09 Released: 2016-07-20
Deposition Author(s): Tsai, Y.C.I., Frankel, P., Fotinou, C., Rana, R., Zachary, I., Djordjevic, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.234 (Depositor), 0.239 (DCC)
R-Value Work:
0.204 (Depositor), 0.211 (DCC)
R-Value Observed:
0.206 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Structural studies of neuropilin-2 reveal a zinc ion binding site remote from the vascular endothelial growth factor binding pocket.

Tsai, Y.C., Fotinou, C., Rana, R., Yelland, T., Frankel, P., Zachary, I., Djordjevic, S.

(2016) FEBS J 283: 1921-1934

PubMed: 26991001 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1111/febs.13711
Primary Citation Related Structures:
5DN2, 5DQ0

PubMed Abstract:
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.

Organizational Affiliation

Institute of Structural and Molecular Biology, University College London, London, UK.

Macromolecule Content

Total Structure Weight: 81.76 kDa
Atom Count: 5,504
Modeled Residue Count: 640
Deposited Residue Count: 708
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neuropilin-2	A, B, C, D	156	Homo sapiens	Mutation(s): 0 Gene Names: NRP2, VEGF165R2
UniProt & NIH Common Fund Data Resources
Find proteins for O60462 (Homo sapiens) Explore O60462 Go to UniProtKB: O60462
PHAROS: O60462 GTEx: ENSG00000118257
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O60462
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Vascular endothelial growth factor A	E [auth F], F [auth G], G [auth E]	28	Homo sapiens	Mutation(s): 0 Gene Names: VEGFA, VEGF
UniProt & NIH Common Fund Data Resources
Find proteins for P15692 (Homo sapiens) Explore P15692 Go to UniProtKB: P15692
PHAROS: P15692 GTEx: ENSG00000112715
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P15692
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B] mmCIF format, chain I [auth B]	I [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]
DIO Query on DIO Download:Ideal Coordinates CCD File SDF format, chain J [auth D] SDF format, chain H [auth B] MOL2 format, chain J [auth D] MOL2 format, chain H [auth B] mmCIF format, chain J [auth D] mmCIF format, chain H [auth B]	H [auth B], J [auth D]	1,4-DIETHYLENE DIOXIDE C₄ H₈ O₂ RYHBNJHYFVUHQT-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Focus chain J [auth D] Interactions & Density Focus chain H [auth B] Focus chain J [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.234 (Depositor), 0.239 (DCC)
R-Value Work: 0.204 (Depositor), 0.211 (DCC)
R-Value Observed: 0.206 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.25	α = 90
b = 139.52	β = 90
c = 106.04	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2016-07-20

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-07-20
Type: Initial release
Version 1.1: 2024-01-10
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-10-16
Changes: Structure summary
Version 1.3: 2026-03-25
Changes: Database references