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Yorodumi- EMDB-0140: Single Particle Cryo-EM map of human Transferrin receptor 1 - H-F... -
+Open data
-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 / Differentiation of keratinocytes in interfollicular epidermis in mammalian skin / : / response to copper ion / response to iron ion ...transferrin receptor activity / negative regulation of mitochondrial fusion / transferrin transport / Transferrin endocytosis and recycling / positive regulation of isotype switching / iron ion sequestering activity / Differentiation of keratinocytes in interfollicular epidermis in mammalian skin / : / response to copper ion / response to iron ion / RND1 GTPase cycle / response to manganese ion / RND2 GTPase cycle / negative regulation of ferroptosis / autolysosome / Scavenging by Class A Receptors / positive regulation of bone resorption / RHOB GTPase cycle / Golgi Associated Vesicle Biogenesis / ferroxidase / RHOC GTPase cycle / RHOJ GTPase cycle / RHOQ GTPase cycle / CDC42 GTPase cycle / RHOH GTPase cycle / RHOG GTPase cycle / transport across blood-brain barrier / intracellular sequestering of iron ion / RHOA GTPase cycle / ferroxidase activity / RAC2 GTPase cycle / RAC3 GTPase cycle / response to nutrient / response to retinoic acid / negative regulation of fibroblast proliferation / positive regulation of T cell proliferation / clathrin-coated pit / positive regulation of B cell proliferation / Hsp70 protein binding / RAC1 GTPase cycle / ferric iron binding / osteoclast differentiation / clathrin-coated endocytic vesicle membrane / cellular response to leukemia inhibitory factor / acute-phase response / Iron uptake and transport / ferrous iron binding / positive regulation of protein-containing complex assembly / HFE-transferrin receptor complex / recycling endosome / receptor internalization / positive regulation of protein localization to nucleus / cellular response to xenobiotic stimulus / recycling endosome membrane / Cargo recognition for clathrin-mediated endocytosis / positive regulation of peptidyl-serine phosphorylation / double-stranded RNA binding / extracellular vesicle / Clathrin-mediated endocytosis / virus receptor activity / melanosome / tertiary granule lumen / positive regulation of NF-kappaB transcription factor activity / positive regulation of canonical NF-kappaB signal transduction / iron ion transport / basolateral plasma membrane / cytoplasmic vesicle / intracellular iron ion homeostasis / ficolin-1-rich granule lumen / blood microparticle / endosome / endosome membrane / early endosome / response to hypoxia / intracellular signal transduction / positive regulation of protein phosphorylation / iron ion binding / immune response / negative regulation of cell population proliferation / external side of plasma membrane / intracellular membrane-bounded organelle / Neutrophil degranulation / positive regulation of gene expression / negative regulation of apoptotic process / protein-containing complex binding / 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 / cytoplasm / cytosol 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 |
-Validation report
Summary document | emd_0140_validation.pdf.gz | 362.3 KB | Display | EMDB validaton report |
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Full document | emd_0140_full_validation.pdf.gz | 361.4 KB | Display | |
Data in XML | emd_0140_validation.xml.gz | 6.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0140 ftp://ftp.pdbj.org/pub/emdb/validation_reports/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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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 |