8IVW

Crystal structure of NRP2 in complex with aNRP2-10 Fab fragment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.21 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.248 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


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

  • DOI: https://doi.org/10.1126/scitranslmed.adf1128
  • Primary Citation of 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.


  • Organizational Affiliation

    aTyr Pharma, San Diego, CA 92121, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Neuropilin-2
A, D, G, J
583Homo sapiensMutation(s): 0 
Gene Names: NRP2VEGF165R2
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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60462
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Heavy chian of antibody 10V8 Fab fragment
B, E, H, K
228Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Light chain of antibody 10V8 Fab fragment
C, F, I, L
215Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.21 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.248 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.424α = 90
b = 225.164β = 91.3
c = 142.996γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-12
    Type: Initial release
  • Version 1.1: 2023-08-23
    Changes: Data collection