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Open data
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Basic information
Entry | Database: PDB / ID: 7t62 | |||||||||
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Title | GPC2 HEP CT3 complex | |||||||||
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![]() | IMMUNE SYSTEM / Glypican-3 complex | |||||||||
Function / homology | ![]() regulation of protein localization to membrane / Defective B3GALT6 causes EDSP2 and SEMDJL1 / Defective B4GALT7 causes EDS, progeroid type / Defective B3GAT3 causes JDSSDHD / Defective EXT2 causes exostoses 2 / Defective EXT1 causes exostoses 1, TRPS2 and CHDS / A tetrasaccharide linker sequence is required for GAG synthesis / HS-GAG biosynthesis / HS-GAG degradation / smoothened signaling pathway ...regulation of protein localization to membrane / Defective B3GALT6 causes EDSP2 and SEMDJL1 / Defective B4GALT7 causes EDS, progeroid type / Defective B3GAT3 causes JDSSDHD / Defective EXT2 causes exostoses 2 / Defective EXT1 causes exostoses 1, TRPS2 and CHDS / A tetrasaccharide linker sequence is required for GAG synthesis / HS-GAG biosynthesis / HS-GAG degradation / smoothened signaling pathway / regulation of signal transduction / Retinoid metabolism and transport / lysosomal lumen / neuron differentiation / positive regulation of neuron projection development / Golgi lumen / cell migration / collagen-containing extracellular matrix / Attachment and Entry / synapse / cell surface / endoplasmic reticulum / extracellular space / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / negative staining / Resolution: 21 Å | |||||||||
![]() | Zhu, J. / Cachau, R. / De Val Alda, N. / Li, N. / Ho, M. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: CAR T cells targeting tumor-associated exons of glypican 2 regress neuroblastoma in mice. Authors: Nan Li / Madeline B Torres / Madeline R Spetz / Ruixue Wang / Luyi Peng / Meijie Tian / Christopher M Dower / Rosa Nguyen / Ming Sun / Chin-Hsien Tai / Natalia de Val / Raul Cachau / Xiaolin ...Authors: Nan Li / Madeline B Torres / Madeline R Spetz / Ruixue Wang / Luyi Peng / Meijie Tian / Christopher M Dower / Rosa Nguyen / Ming Sun / Chin-Hsien Tai / Natalia de Val / Raul Cachau / Xiaolin Wu / Stephen M Hewitt / Rosandra N Kaplan / Javed Khan / Brad St Croix / Carol J Thiele / Mitchell Ho / ![]() Abstract: Targeting solid tumors must overcome several major obstacles, in particular, the identification of elusive tumor-specific antigens. Here, we devise a strategy to help identify tumor-specific epitopes. ...Targeting solid tumors must overcome several major obstacles, in particular, the identification of elusive tumor-specific antigens. Here, we devise a strategy to help identify tumor-specific epitopes. Glypican 2 (GPC2) is overexpressed in neuroblastoma. Using RNA sequencing (RNA-seq) analysis, we show that exon 3 and exons 7-10 of GPC2 are expressed in cancer but are minimally expressed in normal tissues. Accordingly, we discover a monoclonal antibody (CT3) that binds exons 3 and 10 and visualize the complex structure of CT3 and GPC2 by electron microscopy. The potential of this approach is exemplified by designing CT3-derived chimeric antigen receptor (CAR) T cells that regress neuroblastoma in mice. Genomic sequencing of T cells recovered from mice reveals the CAR integration sites that may contribute to CAR T cell proliferation and persistence. These studies demonstrate how RNA-seq data can be exploited to help identify tumor-associated exons that can be targeted by CAR T cell therapies. | |||||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 310.9 KB | Display | ![]() |
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PDB format | ![]() | 258.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 691.9 KB | Display | ![]() |
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Full document | ![]() | 694.3 KB | Display | |
Data in XML | ![]() | 32.9 KB | Display | |
Data in CIF | ![]() | 50.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 25708MC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 61002.066 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#2: Antibody | Mass: 47359.551 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: GPC2 HET CT3 complex / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES |
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Buffer solution | pH: 7.5 |
Specimen | Conc.: 0.01 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: YES / Vitrification applied: NO |
EM staining | Type: NEGATIVE Details: A 3 uL aliquot containing ~0.01 mg/mL of the samples was applied for 20 s onto a carbon-coated 200 Cu mesh grid (Electron Microscopy Sciences, Protochips, Inc.) that had been glow discharged ...Details: A 3 uL aliquot containing ~0.01 mg/mL of the samples was applied for 20 s onto a carbon-coated 200 Cu mesh grid (Electron Microscopy Sciences, Protochips, Inc.) that had been glow discharged at 30 mA for 30 s (Pelco easiGlow, Ted Pella, Inc.), then negatively stained with 0.7% (w/v) uranyl formate for 40 sec. Material: uranyl formate |
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil |
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Electron microscopy imaging
Microscopy | Model: FEI TECNAI 20 |
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Electron gun | Electron source: LAB6 / Accelerating voltage: 200 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 100000 X / Nominal defocus max: 5000 nm / Nominal defocus min: 2000 nm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: FEI EAGLE (2k x 2k) / Num. of real images: 200 |
Image scans | Width: 2048 / Height: 2048 |
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Processing
EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 21000 | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 21 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 21000 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT |