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Yorodumi- EMDB-14874: Cryo-EM Structure of Human Transferrin Receptor 1 bound to DNA Aptamer -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-14874 | |||||||||
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Title | Cryo-EM Structure of Human Transferrin Receptor 1 bound to DNA Aptamer | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information transferrin receptor activity / negative regulation of mitochondrial fusion / transferrin transport / Transferrin endocytosis and recycling / positive regulation of isotype switching / response to iron ion / response to copper ion / response to manganese ion / RND1 GTPase cycle / RND2 GTPase cycle ...transferrin receptor activity / negative regulation of mitochondrial fusion / transferrin transport / Transferrin endocytosis and recycling / positive regulation of isotype switching / response to iron ion / response to copper ion / response to manganese ion / RND1 GTPase cycle / RND2 GTPase cycle / RHOB GTPase cycle / Golgi Associated Vesicle Biogenesis / RHOC GTPase cycle / RHOJ GTPase cycle / RHOQ GTPase cycle / transport across blood-brain barrier / RHOH GTPase cycle / CDC42 GTPase cycle / RHOG GTPase cycle / RHOA GTPase cycle / RAC3 GTPase cycle / RAC2 GTPase cycle / positive regulation of bone resorption / response to retinoic acid / positive regulation of B cell proliferation / clathrin-coated pit / positive regulation of T cell proliferation / RAC1 GTPase cycle / osteoclast differentiation / Hsp70 protein binding / response to nutrient / cellular response to leukemia inhibitory factor / acute-phase response / clathrin-coated endocytic vesicle membrane / positive regulation of protein-containing complex assembly / receptor internalization / HFE-transferrin receptor complex / recycling endosome / positive regulation of protein localization to nucleus / recycling endosome membrane / extracellular vesicle / melanosome / cellular response to xenobiotic stimulus / double-stranded RNA binding / Cargo recognition for clathrin-mediated endocytosis / virus receptor activity / Clathrin-mediated endocytosis / positive regulation of peptidyl-serine phosphorylation / positive regulation of NF-kappaB transcription factor activity / iron ion transport / cytoplasmic vesicle / basolateral plasma membrane / blood microparticle / positive regulation of canonical NF-kappaB signal transduction / intracellular iron ion homeostasis / response to hypoxia / early endosome / endosome membrane / endosome / intracellular signal transduction / positive regulation of protein phosphorylation / external side of plasma membrane / intracellular membrane-bounded organelle / protein-containing complex binding / positive regulation of gene expression / negative regulation of apoptotic process / protein kinase binding / perinuclear region of cytoplasm / cell surface / protein homodimerization activity / extracellular space / RNA binding / extracellular exosome / extracellular region / membrane / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / unidentified (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.54 Å | |||||||||
Authors | Wang T / Bansia H / Gutierrez D / des Georges A | |||||||||
Funding support | United States, 1 items
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Citation | Journal: J Am Chem Soc / Year: 2022 Title: Discovery of a Transferrin Receptor 1-Binding Aptamer and Its Application in Cancer Cell Depletion for Adoptive T-Cell Therapy Manufacturing. Authors: Emmeline L Cheng / Ian I Cardle / Nataly Kacherovsky / Harsh Bansia / Tong Wang / Yunshi Zhou / Jai Raman / Albert Yen / Dominique Gutierrez / Stephen J Salipante / Amédée des Georges / ...Authors: Emmeline L Cheng / Ian I Cardle / Nataly Kacherovsky / Harsh Bansia / Tong Wang / Yunshi Zhou / Jai Raman / Albert Yen / Dominique Gutierrez / Stephen J Salipante / Amédée des Georges / Michael C Jensen / Suzie H Pun / Abstract: The clinical manufacturing of chimeric antigen receptor (CAR) T cells includes cell selection, activation, gene transduction, and expansion. While the method of T-cell selection varies across ...The clinical manufacturing of chimeric antigen receptor (CAR) T cells includes cell selection, activation, gene transduction, and expansion. While the method of T-cell selection varies across companies, current methods do not actively eliminate the cancer cells in the patient's apheresis product from the healthy immune cells. Alarmingly, it has been found that transduction of a single leukemic B cell with the CAR gene can confer resistance to CAR T-cell therapy and lead to treatment failure. In this study, we report the identification of a novel high-affinity DNA aptamer, termed tJBA8.1, that binds transferrin receptor 1 (TfR1), a receptor broadly upregulated by cancer cells. Using competition assays, high resolution cryo-EM, and model building of the aptamer into the resulting electron density, we reveal that tJBA8.1 shares a binding site on TfR1 with holo-transferrin, the natural ligand of TfR1. We use tJBA8.1 to effectively deplete B lymphoma cells spiked into peripheral blood mononuclear cells with minimal impact on the healthy immune cell composition. Lastly, we present opportunities for affinity improvement of tJBA8.1. As TfR1 expression is broadly upregulated in many cancers, including difficult-to-treat T-cell leukemias and lymphomas, our work provides a facile, universal, and inexpensive approach for comprehensively removing cancerous cells from patient apheresis products for safe manufacturing of adoptive T-cell therapies. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_14874.map.gz | 32 MB | EMDB map data format | |
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Header (meta data) | emd-14874-v30.xml emd-14874.xml | 18.8 KB 18.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_14874_fsc.xml | 8.4 KB | Display | FSC data file |
Images | emd_14874.png | 101.4 KB | ||
Others | emd_14874_half_map_1.map.gz emd_14874_half_map_2.map.gz | 59.2 MB 59.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-14874 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14874 | HTTPS FTP |
-Related structure data
Related structure data | 7zqsMC 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_14874.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.8465 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_14874_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_14874_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Human transferrin receptor 1 in complex with DNA aptamer
Entire | Name: Human transferrin receptor 1 in complex with DNA aptamer |
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Components |
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-Supramolecule #1: Human transferrin receptor 1 in complex with DNA aptamer
Supramolecule | Name: Human transferrin receptor 1 in complex with DNA aptamer type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant cell: HEK293 |
Molecular weight | Theoretical: 190 KDa |
-Macromolecule #1: DNA (30-MER)
Macromolecule | Name: DNA (30-MER) / type: dna / ID: 1 / Details: DNA aptamer / Number of copies: 2 / Classification: DNA |
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Source (natural) | Organism: unidentified (others) |
Molecular weight | Theoretical: 15.988172 KDa |
Sequence | String: (DG)(DC)(DA)(DG)(DC)(DA)(DG)(DC)(DG)(DT) (DA)(DA)(DA)(DG)(DG)(DG)(DG)(DG)(DT)(DG) (DT)(DT)(DT)(DG)(DT)(DG)(DC)(DG)(DG) (DT)(DG)(DT)(DG)(DG)(DA)(DG)(DT)(DG)(DC) (DG) (DC)(DG)(DT)(DG)(DC)(DT)(DG)(DC) (DT)(DG)(DC) |
-Macromolecule #2: Transferrin receptor protein 1
Macromolecule | Name: Transferrin receptor protein 1 / type: protein_or_peptide / ID: 2 / Details: Human Transferrin Receptor 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 84.967078 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MMDQARSAFS NLFGGEPLSY TRFSLARQVD GDNSHVEMKL AVDEEENADN NTKANVTKPK RCSGSICYGT IAVIVFFLIG FMIGYLGYC KGVEPKTECE RLAGTESPVR EEPGEDFPAA RRLYWDDLKR KLSEKLDSTD FTGTIKLLNE NSYVPREAGS Q KDENLALY ...String: MMDQARSAFS NLFGGEPLSY TRFSLARQVD GDNSHVEMKL AVDEEENADN NTKANVTKPK RCSGSICYGT IAVIVFFLIG FMIGYLGYC KGVEPKTECE RLAGTESPVR EEPGEDFPAA RRLYWDDLKR KLSEKLDSTD FTGTIKLLNE NSYVPREAGS Q KDENLALY VENQFREFKL SKVWRDQHFV KIQVKDSAQN SVIIVDKNGR LVYLVENPGG YVAYSKAATV TGKLVHANFG TK KDFEDLY TPVNGSIVIV RAGKITFAEK VANAESLNAI GVLIYMDQTK FPIVNAELSF FGHAHLGTGD PYTPGFPSFN HTQ FPPSRS SGLPNIPVQT ISRAAAEKLF GNMEGDCPSD WKTDSTCRMV TSESKNVKLT VSNVLKEIKI LNIFGVIKGF VEPD HYVVV GAQRDAWGPG AAKSGVGTAL LLKLAQMFSD MVLKDGFQPS RSIIFASWSA GDFGSVGATE WLEGYLSSLH LKAFT YINL DKAVLGTSNF KVSASPLLYT LIEKTMQNVK HPVTGQFLYQ DSNWASKVEK LTLDNAAFPF LAYSGIPAVS FCFCED TDY PYLGTTMDTY KELIERIPEL NKVARAAAEV AGQFVIKLTH DVELNLDYER YNSQLLSFVR DLNQYRADIK EMGLSLQ WL YSARGDFFRA TSRLTTDFGN AEKTDRFVMK KLNDRVMRVE YHFLSPYVSP KESPFRHVFW GSGSHTLPAL LENLKLRK Q NNGAFNETLF RNQLALATWT IQGAANALSG DVWDIDNEF |
-Macromolecule #4: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 4 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 2 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7 |
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Grid | Model: EMS Lacey Carbon / Material: COPPER / Mesh: 300 / Support film - #0 - Film type ID: 1 / Support film - #0 - Material: CARBON / Support film - #0 - topology: LACEY / Support film - #1 - Film type ID: 2 / Support film - #1 - Material: CARBON / Support film - #1 - topology: CONTINUOUS / Support film - #1 - Film thickness: 0.30000000000000004 nm / Pretreatment - Type: PLASMA CLEANING |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 37000 |
Sample stage | Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 1397 / Average exposure time: 4.0 sec. / Average electron dose: 79.2 e/Å2 |
-Image processing
-Atomic model buiding 1
Refinement | Protocol: OTHER |
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Output model | PDB-7zqs: |