+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-26720 | |||||||||
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Title | SJ25C1 Fab in complex with soluble CD19 | |||||||||
Map data | SJ25C1 Fab in complex with soluble CD19 | |||||||||
Sample |
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Function / homology | Function and homology information regulation of B cell activation / antigen receptor-mediated signaling pathway / B-1 B cell differentiation / regulation of B cell receptor signaling pathway / B cell proliferation involved in immune response / immunoglobulin mediated immune response / positive regulation of release of sequestered calcium ion into cytosol / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of Complement cascade / B cell receptor signaling pathway ...regulation of B cell activation / antigen receptor-mediated signaling pathway / B-1 B cell differentiation / regulation of B cell receptor signaling pathway / B cell proliferation involved in immune response / immunoglobulin mediated immune response / positive regulation of release of sequestered calcium ion into cytosol / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of Complement cascade / B cell receptor signaling pathway / Constitutive Signaling by Aberrant PI3K in Cancer / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / PIP3 activates AKT signaling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / membrane raft / external side of plasma membrane / protein-containing complex / extracellular exosome / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Mus musculus (house mouse) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Meyerson J / He C | |||||||||
Funding support | 1 items
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Citation | Journal: Sci Immunol / Year: 2023 Title: CD19 CAR antigen engagement mechanisms and affinity tuning. Authors: Changhao He / Jorge Mansilla-Soto / Nandish Khanra / Mohamad Hamieh / Victor Bustos / Alice J Paquette / Andreina Garcia Angus / Derek M Shore / William J Rice / George Khelashvili / Michel ...Authors: Changhao He / Jorge Mansilla-Soto / Nandish Khanra / Mohamad Hamieh / Victor Bustos / Alice J Paquette / Andreina Garcia Angus / Derek M Shore / William J Rice / George Khelashvili / Michel Sadelain / Joel R Meyerson / Abstract: Chimeric antigen receptor (CAR) T cell therapy relies on T cells that are guided by synthetic receptors to target and lyse cancer cells. CARs bind to cell surface antigens through an scFv (binder), ...Chimeric antigen receptor (CAR) T cell therapy relies on T cells that are guided by synthetic receptors to target and lyse cancer cells. CARs bind to cell surface antigens through an scFv (binder), the affinity of which is central to determining CAR T cell function and therapeutic success. CAR T cells targeting CD19 were the first to achieve marked clinical responses in patients with relapsed/refractory B cell malignancies and to be approved by the U.S. Food and Drug Administration (FDA). We report cryo-EM structures of CD19 antigen with the binder FMC63, which is used in four FDA-approved CAR T cell therapies (Kymriah, Yescarta, Tecartus, and Breyanzi), and the binder SJ25C1, which has also been used extensively in multiple clinical trials. We used these structures for molecular dynamics simulations, which guided creation of lower- or higher-affinity binders, and ultimately produced CAR T cells endowed with distinct tumor recognition sensitivities. The CAR T cells exhibited different antigen density requirements to trigger cytolysis and differed in their propensity to prompt trogocytosis upon contacting tumor cells. Our work shows how structural information can be applied to tune CAR T cell performance to specific target antigen densities. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_26720.map.gz | 88.9 MB | EMDB map data format | |
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Header (meta data) | emd-26720-v30.xml emd-26720.xml | 17 KB 17 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_26720_fsc.xml | 11.6 KB | Display | FSC data file |
Images | emd_26720.png | 62.6 KB | ||
Others | emd_26720_half_map_1.map.gz emd_26720_half_map_2.map.gz | 95.4 MB 95.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-26720 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-26720 | HTTPS FTP |
-Validation report
Summary document | emd_26720_validation.pdf.gz | 669.1 KB | Display | EMDB validaton report |
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Full document | emd_26720_full_validation.pdf.gz | 668.7 KB | Display | |
Data in XML | emd_26720_validation.xml.gz | 18.8 KB | Display | |
Data in CIF | emd_26720_validation.cif.gz | 23.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26720 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26720 | HTTPS FTP |
-Related structure data
Related structure data | 7urxMC 7urvC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_26720.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | SJ25C1 Fab in complex with soluble CD19 | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.859 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: SJ25C1 Fab in complex with soluble CD19
File | emd_26720_half_map_1.map | ||||||||||||
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Annotation | SJ25C1 Fab in complex with soluble CD19 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: SJ25C1 Fab in complex with soluble CD19
File | emd_26720_half_map_2.map | ||||||||||||
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Annotation | SJ25C1 Fab in complex with soluble CD19 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : SJ25C1 Fab in complex with soluble CD19
Entire | Name: SJ25C1 Fab in complex with soluble CD19 |
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Components |
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-Supramolecule #1: SJ25C1 Fab in complex with soluble CD19
Supramolecule | Name: SJ25C1 Fab in complex with soluble CD19 / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: all |
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-Supramolecule #2: B-lymphocyte antigen CD19
Supramolecule | Name: B-lymphocyte antigen CD19 / type: complex / ID: 2 / Chimera: Yes / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
-Supramolecule #3: SJ25C1 Fab light chain, SJ25C1 Fab heavy chain
Supramolecule | Name: SJ25C1 Fab light chain, SJ25C1 Fab heavy chain / type: complex / ID: 3 / Chimera: Yes / Parent: 1 / Macromolecule list: #2-#3 |
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Source (natural) | Organism: Mus musculus (house mouse) |
-Macromolecule #1: B-lymphocyte antigen CD19
Macromolecule | Name: B-lymphocyte antigen CD19 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 30.649246 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MPPPRLLFFL LFLTPMEVRP EEPLVVKVEE GDNAVLQCLK GTSDGPTQQL TWSRESPLKP FLKLSLGLPG LGIHVSPLAI WLFISNVSQ QMGGFYLCQP GPPSEKAWQP GWTVNVEGSG ELFRWNVSDL GGLGCGLKNR SSEGPSSPSG KLMSPKLYVW A KDRPEIWE ...String: MPPPRLLFFL LFLTPMEVRP EEPLVVKVEE GDNAVLQCLK GTSDGPTQQL TWSRESPLKP FLKLSLGLPG LGIHVSPLAI WLFISNVSQ QMGGFYLCQP GPPSEKAWQP GWTVNVEGSG ELFRWNVSDL GGLGCGLKNR SSEGPSSPSG KLMSPKLYVW A KDRPEIWE GEPPCLPPRD SLNQSLSQDL TMAPGSTLWL SCGVPPDSVS RGPLSWTHVH PKGPKSLLSL ELKDDRPARD MW VMETGLL LPRATAQDAG KYYCHRGNLT MSFHLEITAR P |
-Macromolecule #2: SJ25C1 Fab light chain
Macromolecule | Name: SJ25C1 Fab light chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 25.765703 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MGWSCIILFL VATATGVHSD IELTQSPKFM STSVGDRVSV TCKASQNVGT NVAWYQQKPG QSPKPLIYSA TYRNSGVPDR FTGSGSGTD FTLTITNVQS KDLADYFCQQ YNRYPYTSGG GTKLEIKRTR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN F YPREAKVQ ...String: MGWSCIILFL VATATGVHSD IELTQSPKFM STSVGDRVSV TCKASQNVGT NVAWYQQKPG QSPKPLIYSA TYRNSGVPDR FTGSGSGTD FTLTITNVQS KDLADYFCQQ YNRYPYTSGG GTKLEIKRTR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN F YPREAKVQ WKVDNALQSG NSQESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC |
-Macromolecule #3: SJ25C1 Fab heavy chain
Macromolecule | Name: SJ25C1 Fab heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 27.030293 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MGWSCIILFL VATATGVHSE VKLQQSGAEL VRPGSSVKIS CKASGYAFSS YWMNWVKQRP GQGLEWIGQI YPGDGDTNYN GKFKGQATL TADKSSSTAY MQLSGLTSED SAVYFCARKT ISSVVDFYFD YWGQGTTVTV SSASTKGPSV FPLAPSSKST S GGTAALGC ...String: MGWSCIILFL VATATGVHSE VKLQQSGAEL VRPGSSVKIS CKASGYAFSS YWMNWVKQRP GQGLEWIGQI YPGDGDTNYN GKFKGQATL TADKSSSTAY MQLSGLTSED SAVYFCARKT ISSVVDFYFD YWGQGTTVTV SSASTKGPSV FPLAPSSKST S GGTAALGC LVKDYFPEPV TVSWNSGALT SGVHTFPAVL QSSGLYSLSS VVTVPSSSLG TQTYICNVNH KPSNTKVDKK VE PKSCHHH HHHHH |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 53.47 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.5 µm |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |