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Yorodumi- EMDB-0046: Single Particle Cryo-EM map of human Transferrin receptor 1 - H-F... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0046 | |||||||||
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Title | Single Particle Cryo-EM map of human Transferrin receptor 1 - H-Ferritin complex at 5.5 Angstrom resolution. | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information transferrin receptor activity / transferrin transport / negative regulation of mitochondrial fusion / Transferrin endocytosis and recycling / positive regulation of isotype switching / iron ion sequestering activity / Differentiation of keratinocytes in interfollicular epidermis in mammalian skin / response to iron ion / response to copper ion / RND1 GTPase cycle ...transferrin receptor activity / transferrin transport / negative regulation of mitochondrial fusion / Transferrin endocytosis and recycling / positive regulation of isotype switching / iron ion sequestering activity / Differentiation of keratinocytes in interfollicular epidermis in mammalian skin / response to iron ion / response to copper ion / RND1 GTPase cycle / response to manganese ion / ferritin complex / RND2 GTPase cycle / negative regulation of ferroptosis / Scavenging by Class A Receptors / RHOB GTPase cycle / Golgi Associated Vesicle Biogenesis / ferroxidase / RHOC GTPase cycle / RHOJ GTPase cycle / autolysosome / RHOQ GTPase cycle / ferroxidase activity / CDC42 GTPase cycle / RHOH GTPase cycle / intracellular sequestering of iron ion / RHOG GTPase cycle / transport across blood-brain barrier / RHOA GTPase cycle / RAC2 GTPase cycle / positive regulation of bone resorption / RAC3 GTPase cycle / response to retinoic acid / negative regulation of fibroblast proliferation / clathrin-coated pit / positive regulation of B cell proliferation / positive regulation of T cell proliferation / RAC1 GTPase cycle / Hsp70 protein binding / autophagosome / ferric iron binding / osteoclast differentiation / response to nutrient / cellular response to leukemia inhibitory factor / acute-phase response / Iron uptake and transport / clathrin-coated endocytic vesicle membrane / ferrous iron binding / positive regulation of protein-containing complex assembly / HFE-transferrin receptor complex / receptor internalization / recycling endosome / positive regulation of protein localization to nucleus / multicellular organismal-level iron ion homeostasis / recycling endosome membrane / double-stranded RNA binding / melanosome / extracellular vesicle / cellular response to xenobiotic stimulus / tertiary granule lumen / Cargo recognition for clathrin-mediated endocytosis / positive regulation of peptidyl-serine phosphorylation / Clathrin-mediated endocytosis / positive regulation of NF-kappaB transcription factor activity / virus receptor activity / iron ion transport / cytoplasmic vesicle / basolateral plasma membrane / positive regulation of canonical NF-kappaB signal transduction / intracellular iron ion homeostasis / blood microparticle / ficolin-1-rich granule lumen / early endosome / response to hypoxia / endosome membrane / intracellular signal transduction / endosome / immune response / iron ion binding / positive regulation of protein phosphorylation / negative regulation of cell population proliferation / external side of plasma membrane / intracellular membrane-bounded organelle / Neutrophil degranulation / positive regulation of gene expression / protein-containing complex binding / negative regulation of apoptotic process / protein kinase binding / perinuclear region of cytoplasm / cell surface / protein homodimerization activity / RNA binding / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / nucleus / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.5 Å | |||||||||
Authors | Testi C / Montemiglio LC / Vallone B / Des Georges A / Boffi A / Mancia F / Baiocco P | |||||||||
Citation | Journal: Nat Commun / Year: 2019 Title: Cryo-EM structure of the human ferritin-transferrin receptor 1 complex. Authors: Linda Celeste Montemiglio / Claudia Testi / Pierpaolo Ceci / Elisabetta Falvo / Martina Pitea / Carmelinda Savino / Alessandro Arcovito / Giovanna Peruzzi / Paola Baiocco / Filippo Mancia / ...Authors: Linda Celeste Montemiglio / Claudia Testi / Pierpaolo Ceci / Elisabetta Falvo / Martina Pitea / Carmelinda Savino / Alessandro Arcovito / Giovanna Peruzzi / Paola Baiocco / Filippo Mancia / Alberto Boffi / Amédée des Georges / Beatrice Vallone / Abstract: Human transferrin receptor 1 (CD71) guarantees iron supply by endocytosis upon binding of iron-loaded transferrin and ferritin. Arenaviruses and the malaria parasite exploit CD71 for cell invasion ...Human transferrin receptor 1 (CD71) guarantees iron supply by endocytosis upon binding of iron-loaded transferrin and ferritin. Arenaviruses and the malaria parasite exploit CD71 for cell invasion and epitopes on CD71 for interaction with transferrin and pathogenic hosts were identified. Here, we provide the molecular basis of the CD71 ectodomain-human ferritin interaction by determining the 3.9 Å resolution single-particle cryo-electron microscopy structure of their complex and by validating our structural findings in a cellular context. The contact surfaces between the heavy-chain ferritin and CD71 largely overlap with arenaviruses and Plasmodium vivax binding regions in the apical part of the receptor ectodomain. Our data account for transferrin-independent binding of ferritin to CD71 and suggest that select pathogens may have adapted to enter cells by mimicking the ferritin access gate. | |||||||||
History |
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-Structure visualization
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
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Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_0046.map.gz | 59.5 MB | EMDB map data format | |
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Header (meta data) | emd-0046-v30.xml emd-0046.xml | 11.6 KB 11.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_0046_fsc.xml | 10.7 KB | Display | FSC data file |
Images | emd_0046.png | 283.9 KB | ||
Masks | emd_0046_msk_1.map | 64 MB | Mask map | |
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0046 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0046 | HTTPS FTP |
-Validation report
Summary document | emd_0046_validation.pdf.gz | 304.9 KB | Display | EMDB validaton report |
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Full document | emd_0046_full_validation.pdf.gz | 304 KB | Display | |
Data in XML | emd_0046_validation.xml.gz | 10.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0046 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0046 | HTTPS FTP |
-Related structure data
Related structure data | 6gsrMC 0140C 6h5iC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_0046.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: 1.33 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_0046_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Complex of human Transferrin Receptor 1 and human H-chain Ferritin
Entire | Name: Complex of human Transferrin Receptor 1 and human H-chain Ferritin |
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Components |
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-Supramolecule #1: Complex of human Transferrin Receptor 1 and human H-chain Ferritin
Supramolecule | Name: Complex of human Transferrin Receptor 1 and human H-chain Ferritin type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 675 KDa |
-Macromolecule #1: Ferritin heavy chain
Macromolecule | Name: Ferritin heavy chain / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: TSQVRQNYHQ DSEAAINRQI NLELYASYVY LSMSYYFDRD DVALKNFAKY FLHQSHEERE HAEKLMKLQN QRGGRIFLQD IKKPDCDDW ESGLNAMECA LHLEKNVNQS LLELHKLATD KNDPHLCDFI ETHYLNEQVK AIKELGDHVT NLRKMGAPES G LAEYLFDK HTLG |
-Macromolecule #2: human Transferrin Receptor 1
Macromolecule | Name: human Transferrin Receptor 1 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: LYWDDLKRKL SEKLDSTDFT STIKLLNENS YVPREAGSQK DENLALYVEN EFREFKLSKV WRDQHFVKIQ VKDSAQNSVI IVDKNGRLV YLVENPGGYV AYSKAATVTG KLVHANFGTK KDFEDLYTPV NGSIVIVRAG KITFAEKVAN AESLNAIGVL I YMDQTKFP ...String: LYWDDLKRKL SEKLDSTDFT STIKLLNENS YVPREAGSQK DENLALYVEN EFREFKLSKV WRDQHFVKIQ VKDSAQNSVI IVDKNGRLV YLVENPGGYV AYSKAATVTG KLVHANFGTK KDFEDLYTPV NGSIVIVRAG KITFAEKVAN AESLNAIGVL I YMDQTKFP IVNAELSFFG HAHLGTGDPY TPGFPSFNHT QFPPSRSSGL PNIPVQTISR AAAEKLFGNM EGDCPSDWKT DS TCRMVTS ESKNVKLTVS NVLKEIKILN IFGVIKGFVE PDHYVVVGAQ RDAWGPGAAK SGVGTALLLK LAQMFSDMVL KDG FQPSRS IIFASWSAGD FGSVGATEWL EGYLSSLHLK AFTYINLDKA VLGTSNFKVS ASPLLYTLIE KTMQNVKHPV TGQF LYQDS NWASKVEKLT LDNAAFPFLA YSGIPAVSFC FCEDTDYPYL GTTMDTYKEL IERIPELNKV ARAAAEVAGQ FVIKL THDV ELNLDYEEYN SQLLSFVRDL NQYRADIKEM GLSLQWLYSA RGDFFRATSR LTTDFGNAEK TDRFVMKKLN DRVMRV EYH FLSPYVSPKE SPFRHVFWGS GSHTLPALLE NLKLRKQNNG AFNETLFRNQ LALATWTIQG AANALSGDVW DIDNEF |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.2 mg/mL |
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Buffer | pH: 7.2 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: OTHER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Protocol: RIGID BODY FIT |
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Output model | PDB-6gsr: |