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Yorodumi- EMDB-0140: Single Particle Cryo-EM map of human Transferrin receptor 1 - H-F... -
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-Basic information
Entry | Database: EMDB / ID: EMD-0140 | |||||||||
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Title | Single Particle Cryo-EM map of human Transferrin receptor 1 - H-Ferritin complex. | |||||||||
Map data | Map at 3.9 A of the human CD71 receptor and human H-Ferritin | |||||||||
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 / iron ion sequestering activity / Scavenging by Class A Receptors / intracellular ferritin complex / response to iron ion / response to copper ion ...transferrin receptor activity / negative regulation of mitochondrial fusion / transferrin transport / Transferrin endocytosis and recycling / positive regulation of isotype switching / iron ion sequestering activity / Scavenging by Class A Receptors / intracellular ferritin complex / response to iron ion / response to copper ion / response to manganese ion / RND1 GTPase cycle / RND2 GTPase cycle / autolysosome / RHOB GTPase cycle / Golgi Associated Vesicle Biogenesis / ferroxidase / RHOJ GTPase cycle / RHOC GTPase cycle / RHOQ GTPase cycle / intracellular sequestering of iron ion / ferroxidase activity / RHOH GTPase cycle / CDC42 GTPase cycle / transport across blood-brain barrier / 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 / negative regulation of fibroblast proliferation / clathrin-coated pit / Hsp70 protein binding / positive regulation of T cell proliferation / RAC1 GTPase cycle / cellular response to leukemia inhibitory factor / ferric iron binding / osteoclast differentiation / response to nutrient / acute-phase response / positive regulation of protein-containing complex assembly / ferrous iron binding / clathrin-coated endocytic vesicle membrane / Iron uptake and transport / 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 / tertiary granule lumen / 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 / ficolin-1-rich granule lumen / response to hypoxia / early endosome / endosome membrane / endosome / intracellular signal transduction / immune response / positive regulation of protein phosphorylation / iron ion binding / negative regulation of cell population proliferation / external side of plasma membrane / intracellular membrane-bounded organelle / Neutrophil degranulation / 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 / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
Authors | Testi C / Montemiglio LC / Vallone B / Des Georges A / Boffi A / Mancia F / Baiocco P / Savino C | |||||||||
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
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_0140.map.gz | 59.4 MB | EMDB map data format | |
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Header (meta data) | emd-0140-v30.xml emd-0140.xml | 14.1 KB 14.1 KB | Display Display | EMDB header |
Images | emd_0140.png | 88.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0140 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0140 | HTTPS FTP |
-Related structure data
Related structure data | 6h5iMC 0046C 6gsrC 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_0140.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Map at 3.9 A of the human CD71 receptor and human H-Ferritin | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.33 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Complex of the ectodomain of human Transferrin Receptor 1 and H-c...
Entire | Name: Complex of the ectodomain of human Transferrin Receptor 1 and H-chain Ferritin |
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Components |
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-Supramolecule #1: Complex of the ectodomain of human Transferrin Receptor 1 and H-c...
Supramolecule | Name: Complex of the ectodomain of human Transferrin Receptor 1 and H-chain Ferritin type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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-Supramolecule #2: C H-chain Ferritin
Supramolecule | Name: C H-chain Ferritin / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Supramolecule #3: Ectodomain of human Transferrin Receptor 1
Supramolecule | Name: Ectodomain of human Transferrin Receptor 1 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) |
-Macromolecule #1: Ferritin heavy chain
Macromolecule | Name: Ferritin heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 24 / Enantiomer: LEVO / EC number: ferroxidase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 20.116547 KDa |
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: Transferrin receptor protein 1
Macromolecule | Name: Transferrin receptor protein 1 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 71.807258 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: RLYWDDLKRK LSEKLDSTDF TSTIKLLNEN SYVPREAGSQ KDENLALYVE NQFREFKLSK VWRDQHFVKI QVKDSAQNSV IIVDKNGRL VYLVENPGGY VAYSKAATVT GKLVHANFGT KKDFEDLYTP VNGSIVIVRA GKITFAEKVA NAESLNAIGV L IYMDQTKF ...String: RLYWDDLKRK LSEKLDSTDF TSTIKLLNEN SYVPREAGSQ KDENLALYVE NQFREFKLSK VWRDQHFVKI QVKDSAQNSV IIVDKNGRL VYLVENPGGY VAYSKAATVT GKLVHANFGT KKDFEDLYTP VNGSIVIVRA GKITFAEKVA NAESLNAIGV L IYMDQTKF PIVNAELSFF GHAHLGTGDP YTPGFPSFNH TQFPPSRSSG LPNIPVQTIS RAAAEKLFGN MEGDCPSDWK TD STCRMVT SESKNVKLTV SNVLKEIKIL NIFGVIKGFV EPDHYVVVGA QRDAWGPGAA KSGVGTALLL KLAQMFSDMV LKD GFQPSR SIIFASWSAG DFGSVGATEW LEGYLSSLHL KAFTYINLDK AVLGTSNFKV SASPLLYTLI EKTMQNVKHP VTGQ FLYQD SNWASKVEKL TLDNAAFPFL AYSGIPAVSF CFCEDTDYPY LGTTMDTYKE LIERIPELNK VARAAAEVAG QFVIK LTHD VELNLDYERY NSQLLSFVRD LNQYRADIKE MGLSLQWLYS ARGDFFRATS RLTTDFGNAE KTDRFVMKKL NDRVMR VEY HFLSPYVSPK ESPFRHVFWG SGSHTLPALL ENLKLRKQNN GAFNETLFRN QLALATWTIQ GAANALSGDV WDIDNEF |
-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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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: OTHER |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 40.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 73700 |
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CTF correction | Software - Name: Gctf |
Startup model | Type of model: EMDB MAP EMDB ID: |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final 3D classification | Number classes: 8 / Software - Name: RELION |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Number classes used: 3 / Applied symmetry - Point group: O (octahedral) / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 53878 |