6WJL

Crystal structure of Glypican-2 core protein in complex with D3 Fab


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.317 
  • R-Value Work: 0.278 
  • R-Value Observed: 0.279 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A GPC2 antibody-drug conjugate is efficacious against neuroblastoma and small-cell lung cancer via binding a conformational epitope.

Raman, S.Buongervino, S.N.Lane, M.V.Zhelev, D.V.Zhu, Z.Cui, H.Martinez, B.Martinez, D.Wang, Y.Upton, K.Patel, K.Rathi, K.S.Navia, C.T.Harmon, D.B.Li, Y.Pawel, B.Dimitrov, D.S.Maris, J.M.Julien, J.P.Bosse, K.R.

(2021) Cell Rep Med 2: 100344-100344

  • DOI: 10.1016/j.xcrm.2021.100344
  • Primary Citation of Related Structures:  
    6WJL

  • PubMed Abstract: 
  • Glypican 2 (GPC2) is a MYCN-regulated, differentially expressed cell-surface oncoprotein and target for immune-based therapies in neuroblastoma. Here, we build on GPC2's immunotherapeutic attributes by finding that it is also a highly expressed, MYCN-driven oncoprotein on small-cell lung cancers (SCLCs), with significantly enriched expression in both the SCLC and neuroblastoma stem cell compartment ...

    Glypican 2 (GPC2) is a MYCN-regulated, differentially expressed cell-surface oncoprotein and target for immune-based therapies in neuroblastoma. Here, we build on GPC2's immunotherapeutic attributes by finding that it is also a highly expressed, MYCN-driven oncoprotein on small-cell lung cancers (SCLCs), with significantly enriched expression in both the SCLC and neuroblastoma stem cell compartment.By solving the crystal structure of the D3-GPC2-Fab/GPC2 complex at 3.3 Å resolution, we further illustrate that the GPC2-directed antibody-drug conjugate (ADC; D3-GPC2-PBD), that links a human GPC2 antibody (D3) to DNA-damaging pyrrolobenzodiazepine (PBD) dimers, binds a tumor-specific, conformation-dependent epitope of the core GPC2 extracellular domain. We then show that this ADC induces durable neuroblastoma and SCLC tumor regression via induction of DNA damage, apoptosis, and bystander cell killing, notably with no signs of ADC-induced in vivo toxicity. These studies provide preclinical data to support the clinical translation of ADCs targeting GPC2.


    Organizational Affiliation

    Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glypican-2E,
A [auth G]
482Homo sapiensMutation(s): 3 
Gene Names: GPC2
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N158 (Homo sapiens)
Explore Q8N158 
Go to UniProtKB:  Q8N158
PHAROS:  Q8N158
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UniProt GroupQ8N158
Protein Feature View
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
D3 Fab Heavy chainF,
B [auth H]
220Homo sapiensMutation(s): 0 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
VHH domainG [auth I],
C [auth K]
121Lama glamaMutation(s): 0 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
D3 Fab Light ChainH [auth J],
D [auth L]
214Homo sapiensMutation(s): 0 
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.317 
  • R-Value Work: 0.278 
  • R-Value Observed: 0.279 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.942α = 90
b = 225.646β = 104.75
c = 107.25γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XPREPdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)ACB-12002
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)AGM-12006

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-21
    Type: Initial release
  • Version 1.1: 2021-04-28
    Changes: Derived calculations
  • Version 1.2: 2021-11-17
    Changes: Database references