8IVX | pdb_00008ivx

Crystal structure of NRP2 in complex with aNRP2-14 Fab fragment

• PDB DOI: https://doi.org/10.2210/pdb8IVX/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2023-03-29 Released: 2023-07-12 
• Deposition Author(s): Geng, Y., Zhai, L.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.225 (Depositor), 0.231 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Starting Model: experimental

Literature

Inhibition of VEGF binding to neuropilin-2 enhances chemosensitivity and inhibits metastasis in triple-negative breast cancer.

Xu, Z., Goel, H.L., Burkart, C., Burman, L., Chong, Y.E., Barber, A.G., Geng, Y., Zhai, L., Wang, M., Kumar, A., Menefee, A., Polizzi, C., Eide, L., Rauch, K., Rahman, J., Hamel, K., Fogassy, Z., Klopp-Savino, S., Paz, S., Zhang, M., Cubitt, A., Nangle, L.A., Mercurio, A.M.

(2023) Sci Transl Med 15: eadf1128-eadf1128

• PubMed: 37134152 
• DOI: https://doi.org/10.1126/scitranslmed.adf1128
• Primary Citation Related Structures: 
  8IVW, 8IVX


• PubMed Abstract: 
  

  Although blocking the binding of vascular endothelial growth factor (VEGF) to neuropilin-2 (NRP2) on tumor cells is a potential strategy to treat aggressive carcinomas, a lack of effective reagents that can be used clinically has hampered this potential therapy. Here, we describe the generation of a fully humanized, high-affinity monoclonal antibody (aNRP2-10) that specifically inhibits the binding of VEGF to NRP2, conferring antitumor activity without causing toxicity. Using triple-negative breast cancer as a model, we demonstrated that aNRP2-10 could be used to isolate cancer stem cells (CSCs) from heterogeneous tumor populations and inhibit CSC function and epithelial-to-mesenchymal transition. aNRP2-10 sensitized cell lines, organoids, and xenografts to chemotherapy and inhibited metastasis by promoting the differentiation of CSCs to a state that is more responsive to chemotherapy and less prone to metastasis. These data provide justification for the initiation of clinical trials designed to improve the response of patients with aggressive tumors to chemotherapy using this monoclonal antibody.

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Organizational Affiliation: 
• aTyr Pharma, San Diego, CA 92121, USA.
Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA.
IAS HKUST - Scripps R&D Laboratory, Institute for Advanced Study, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China.
Pangu Biopharma, 26th Floor, Three Exchange Square, 8 Connaught Place, Central, Hong Kong, China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 114.54 kDa 
• Atom Count: 6,954 
• Modeled Residue Count: 835 
• Deposited Residue Count: 1,029 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
aNRP2-14	A	583	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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain of antibody 14V4 Fab fragment	B [auth H]	231	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain of antibody 14V4 Fab fragment	C [auth L]	215	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	D [auth H]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.225 (Depositor), 0.231 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.501	α = 90
b = 89.411	β = 94.18
c = 130.877	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-07-12 
Deposition Author(s): Geng, Y., Zhai, L.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-07-12
  Type: Initial release
  
• Version 1.1: 2023-08-23
  Changes: Data collection
• Version 1.2: 2024-11-20
  Changes: Structure summary