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Yorodumi- PDB-6h5i: Single Particle Cryo-EM map of human Transferrin receptor 1 - H-F... -
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-Basic information
Entry | Database: PDB / ID: 6h5i | ||||||
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Title | Single Particle Cryo-EM map of human Transferrin receptor 1 - H-Ferritin complex. | ||||||
Components |
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Keywords | METAL BINDING PROTEIN / Transferrin Receptor 1 / Ferritin / Complex / Single Particle Cryo-EM | ||||||
Function / homology | Function and homology information transferrin receptor activity / negative regulation of mitochondrial fusion / transferrin transport / Transferrin endocytosis and recycling / Differentiation of keratinocytes in interfollicular epidermis in mammalian skin / positive regulation of isotype switching / iron ion sequestering activity / : / response to copper ion / response to iron ion ...transferrin receptor activity / negative regulation of mitochondrial fusion / transferrin transport / Transferrin endocytosis and recycling / Differentiation of keratinocytes in interfollicular epidermis in mammalian skin / positive regulation of isotype switching / iron ion sequestering activity / : / response to copper ion / response to iron ion / RND1 GTPase cycle / response to manganese ion / RND2 GTPase cycle / autolysosome / Scavenging by Class A Receptors / RHOB GTPase cycle / Golgi Associated Vesicle Biogenesis / ferroxidase / RHOJ GTPase cycle / RHOC GTPase cycle / RHOQ GTPase cycle / CDC42 GTPase cycle / RHOH GTPase cycle / transport across blood-brain barrier / RHOG GTPase cycle / RHOA GTPase cycle / intracellular sequestering of iron ion / ferroxidase activity / RAC2 GTPase cycle / RAC3 GTPase cycle / positive regulation of bone resorption / response to retinoic acid / clathrin-coated pit / positive regulation of T cell proliferation / negative regulation of fibroblast proliferation / positive regulation of B cell proliferation / Hsp70 protein binding / RAC1 GTPase cycle / ferric iron binding / response to nutrient / osteoclast differentiation / cellular response to leukemia inhibitory factor / acute-phase response / Iron uptake and transport / clathrin-coated endocytic vesicle membrane / positive regulation of protein-containing complex assembly / ferrous iron binding / HFE-transferrin receptor complex / recycling endosome / receptor internalization / positive regulation of protein localization to nucleus / recycling endosome membrane / double-stranded RNA binding / extracellular vesicle / melanosome / cellular response to xenobiotic stimulus / Cargo recognition for clathrin-mediated endocytosis / tertiary granule lumen / positive regulation of peptidyl-serine phosphorylation / Clathrin-mediated endocytosis / virus receptor activity / positive regulation of NF-kappaB transcription factor activity / iron ion transport / cytoplasmic vesicle / basolateral plasma membrane / positive regulation of canonical NF-kappaB signal transduction / intracellular iron ion homeostasis / ficolin-1-rich granule lumen / early endosome / blood microparticle / response to hypoxia / endosome membrane / intracellular signal transduction / endosome / iron ion binding / positive regulation of protein phosphorylation / immune response / 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å | ||||||
Authors | Testi, C. / Montemiglio, L.C. / 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 |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6h5i.cif.gz | 1002.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6h5i.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6h5i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6h5i_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6h5i_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6h5i_validation.xml.gz | 121.3 KB | Display | |
Data in CIF | 6h5i_validation.cif.gz | 189.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h5/6h5i ftp://data.pdbj.org/pub/pdb/validation_reports/h5/6h5i | HTTPS FTP |
-Related structure data
Related structure data | 0140MC 0046C 6gsrC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 20116.547 Da / Num. of mol.: 24 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FTH1, FTH, FTHL6, OK/SW-cl.84, PIG15 / Production host: Escherichia coli (E. coli) / References: UniProt: P02794, ferroxidase #2: Protein | Mass: 71807.258 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TFRC / Production host: Homo sapiens (human) / References: UniProt: P02786 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
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Buffer solution | pH: 7.2 | ||||||||||||||||||||||||
Specimen | Conc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: OTHER |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.13_2998: / Classification: refinement | ||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 73700 | ||||||||||||||||||||||||||||
Symmetry | Point symmetry: O (octahedral) | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 53878 / Num. of class averages: 3 / Symmetry type: POINT | ||||||||||||||||||||||||||||
Atomic model building | Protocol: OTHER | ||||||||||||||||||||||||||||
Atomic model building |
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