[English] 日本語
Yorodumi
- EMDB-14874: Cryo-EM Structure of Human Transferrin Receptor 1 bound to DNA Aptamer -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-14874
TitleCryo-EM Structure of Human Transferrin Receptor 1 bound to DNA Aptamer
Map data
Sample
  • Complex: Human transferrin receptor 1 in complex with DNA aptamer
    • DNA: DNA (30-MER)
    • Protein or peptide: Transferrin receptor protein 1
  • Ligand: MAGNESIUM ION
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
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
Transferrin receptor protein 1/2, PA domain / Transferrin receptor-like, dimerisation domain / Transferrin receptor-like, dimerisation domain superfamily / Glutamate carboxypeptidase 2-like / Transferrin receptor-like dimerisation domain / PA domain superfamily / PA domain / PA domain / Peptidase M28 / Peptidase family M28
Similarity search - Domain/homology
Transferrin receptor protein 1
Similarity search - Component
Biological speciesHomo sapiens (human) / unidentified (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.54 Å
AuthorsWang T / Bansia H / Gutierrez D / des Georges A
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM133598 United States
CitationJournal: 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
DepositionMay 2, 2022-
Header (metadata) releaseAug 17, 2022-
Map releaseAug 17, 2022-
UpdateAug 17, 2022-
Current statusAug 17, 2022Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_14874.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 256 pix.
= 216.704 Å
0.85 Å/pix.
x 256 pix.
= 216.704 Å
0.85 Å/pix.
x 256 pix.
= 216.704 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8465 Å
Density
Contour LevelBy AUTHOR: 0.16
Minimum - Maximum-0.17244233 - 0.592307
Average (Standard dev.)0.0043409267 (±0.022970878)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 216.704 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_14874_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Half map: #1

Fileemd_14874_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Sample components

-
Entire : Human transferrin receptor 1 in complex with DNA aptamer

EntireName: Human transferrin receptor 1 in complex with DNA aptamer
Components
  • Complex: Human transferrin receptor 1 in complex with DNA aptamer
    • DNA: DNA (30-MER)
    • Protein or peptide: Transferrin receptor protein 1
  • Ligand: MAGNESIUM ION
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

-
Supramolecule #1: Human transferrin receptor 1 in complex with DNA aptamer

SupramoleculeName: Human transferrin receptor 1 in complex with DNA aptamer
type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK293
Molecular weightTheoretical: 190 KDa

-
Macromolecule #1: DNA (30-MER)

MacromoleculeName: DNA (30-MER) / type: dna / ID: 1 / Details: DNA aptamer / Number of copies: 2 / Classification: DNA
Source (natural)Organism: unidentified (others)
Molecular weightTheoretical: 15.988172 KDa
SequenceString:
(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

MacromoleculeName: Transferrin receptor protein 1 / type: protein_or_peptide / ID: 2 / Details: Human Transferrin Receptor 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 84.967078 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 4 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 2 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7
GridModel: 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
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 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 stageSpecimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Cooling holder cryogen: NITROGEN
Image recordingFilm 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

Startup modelType of model: OTHER / Details: Ab-initio
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.54 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 216817
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementProtocol: OTHER
Output model

PDB-7zqs:
Cryo-EM Structure of Human Transferrin Receptor 1 bound to DNA Aptamer

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more