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Open data
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Basic information
Entry | Database: PDB / ID: 1suv | ||||||
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Title | Structure of Human Transferrin Receptor-Transferrin Complex | ||||||
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![]() | METAL TRANSPORT / Protein Complex | ||||||
Function / homology | ![]() transferrin receptor activity / negative regulation of mitochondrial fusion / transferrin transport / iron chaperone activity / Transferrin endocytosis and recycling / transferrin receptor binding / positive regulation of isotype switching / basal part of cell / positive regulation of cell motility / response to copper ion ...transferrin receptor activity / negative regulation of mitochondrial fusion / transferrin transport / iron chaperone activity / Transferrin endocytosis and recycling / transferrin receptor binding / positive regulation of isotype switching / basal part of cell / positive regulation of cell motility / response to copper ion / response to iron ion / response to manganese ion / RND1 GTPase cycle / RND2 GTPase cycle / RHOB GTPase cycle / Golgi Associated Vesicle Biogenesis / RHOJ GTPase cycle / RHOC GTPase cycle / RHOQ GTPase cycle / CDC42 GTPase cycle / RHOH GTPase cycle / transport across blood-brain barrier / RHOG GTPase cycle / endocytic vesicle / RHOA GTPase cycle / RAC2 GTPase cycle / RAC3 GTPase cycle / positive regulation of bone resorption / response to retinoic acid / positive regulation of T cell proliferation / clathrin-coated pit / positive regulation of phosphorylation / positive regulation of B cell proliferation / Hsp70 protein binding / RAC1 GTPase cycle / ERK1 and ERK2 cascade / response to nutrient / ferric iron binding / osteoclast differentiation / basal plasma membrane / cellular response to leukemia inhibitory factor / acute-phase response / cellular response to iron ion / actin filament organization / Iron uptake and transport / Post-translational protein phosphorylation / clathrin-coated endocytic vesicle membrane / positive regulation of protein-containing complex assembly / regulation of protein stability / ferrous iron binding / regulation of iron ion transport / HFE-transferrin receptor complex / receptor internalization / recycling endosome / positive regulation of receptor-mediated endocytosis / positive regulation of protein localization to nucleus / recycling endosome membrane / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / double-stranded RNA binding / extracellular vesicle / melanosome / cellular response to xenobiotic stimulus / late endosome / Cargo recognition for clathrin-mediated endocytosis / Platelet degranulation / positive regulation of peptidyl-serine phosphorylation / Clathrin-mediated endocytosis / virus receptor activity / positive regulation of NF-kappaB transcription factor activity / iron ion transport / antibacterial humoral response / cytoplasmic vesicle / basolateral plasma membrane / secretory granule lumen / positive regulation of canonical NF-kappaB signal transduction / intracellular iron ion homeostasis / vesicle / early endosome / blood microparticle / endosome membrane / response to hypoxia / intracellular signal transduction / endosome / positive regulation of protein phosphorylation / apical plasma membrane / endoplasmic reticulum lumen / 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 / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / cell surface / protein homodimerization activity / RNA binding / extracellular space / extracellular exosome / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.5 Å | ||||||
![]() | Cheng, Y. / Zak, O. / Aisen, P. / Harrison, S.C. / Walz, T. | ||||||
![]() | ![]() Title: Structure of the human transferrin receptor-transferrin complex. Authors: Yifan Cheng / Olga Zak / Philip Aisen / Stephen C Harrison / Thomas Walz / ![]() Abstract: Iron, insoluble as free Fe(3+) and toxic as free Fe(2+), is distributed through the body as Fe(3+) bound to transferrin (Tf) for delivery to cells by endocytosis of its complex with transferrin ...Iron, insoluble as free Fe(3+) and toxic as free Fe(2+), is distributed through the body as Fe(3+) bound to transferrin (Tf) for delivery to cells by endocytosis of its complex with transferrin receptor (TfR). Although much is understood of the transferrin endocytotic cycle, little has been uncovered of the molecular details underlying the formation of the receptor-transferrin complex. Using cryo-electron microscopy, we have produced a density map of the TfR-Tf complex at subnanometer resolution. An atomic model, obtained by fitting crystal structures of diferric Tf and the receptor ectodomain into the map, shows that the Tf N-lobe is sandwiched between the membrane and the TfR ectodomain and that the C-lobe abuts the receptor helical domain. When Tf binds receptor, its N-lobe moves by about 9 A with respect to its C-lobe. The structure of TfR-Tf complex helps account for known differences in the iron-release properties of free and receptor bound Tf. | ||||||
History |
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Remark 999 | SEQUENCE NOT ALL THE CHAINS IN THE MODEL ARE HUMAN, ALTHOUGH THE PROTEINS USED TO DETERMINE THE 7.5 ...SEQUENCE NOT ALL THE CHAINS IN THE MODEL ARE HUMAN, ALTHOUGH THE PROTEINS USED TO DETERMINE THE 7.5 A STRUCTURE OF THE TFR-TF COMPLEX WERE ALL HUMAN. THE AUTHORS CREATED THE MODEL BY FITTING X-RAY CRYSTAL STRUCTURES INTO THEIR 7.5 A EM DENSITY MAP. SINCE THERE IS NO STRUCTURE FOR THE HUMAN TRANSFERRIN C-LOBE, THE AUTHORS OPTED TO USE THE C-LOBE FROM RABBIT TF (1JNF). THE OTHER TWO CHAINS ARE HUMAN (1CX8 - HUMAN TFR AND 1A8E - HUMAN TF N-LOBE). THE CHAINS E AND F MATCH SWS P19134, A RABBIT SOURCE. REGARDING THE CONFLICTS: BOTH SEQUENCE AND COORDINATES ARE FROM THE ORIGINAL PDB-FILES AND THE AUTHORS DID NOT MAKE ANY MODIFICATIONS TO IT. |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 504.4 KB | Display | ![]() |
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PDB format | ![]() | 422 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 411.8 KB | Display | ![]() |
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Full document | ![]() | 544 KB | Display | |
Data in XML | ![]() | 69.5 KB | Display | |
Data in CIF | ![]() | 98.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Symmetry | Point symmetry: (Schoenflies symbol: C2 (2 fold cyclic)) |
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Components
#1: Protein | Mass: 71622.961 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 36408.414 Da / Num. of mol.: 2 / Fragment: repeat 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Protein | Mass: 38300.445 Da / Num. of mol.: 2 / Fragment: repeat 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #4: Chemical | ChemComp-CO3 / #5: Chemical | ChemComp-FE / |
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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 |
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Sample preparation
Component | Name: Human Transferrin Receptor - Transferrin Complex / Type: COMPLEX |
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Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Tecnai F20 / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI F20 / Date: Oct 15, 2001 |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 50000 X / Calibrated magnification: 51160 X / Nominal defocus max: 5000 nm / Nominal defocus min: 2500 nm / Cs: 2 mm |
Specimen holder | Temperature: 93 K / Tilt angle max: 0 ° / Tilt angle min: 0 ° |
Image recording | Electron dose: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM |
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Processing
CTF correction | Details: CTF correction for each particle | ||||||||||||
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Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||
3D reconstruction | Method: Fourier Space reconstruction / Resolution: 7.5 Å / Nominal pixel size: 2.8 Å / Actual pixel size: 2.74 Å / Details: using program FREALIGN / Symmetry type: POINT | ||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL Target criteria: visual fit using program O followed by rigid body refinement using program MAVE Details: REFINEMENT PROTOCOL--rigid body | ||||||||||||
Atomic model building |
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Refinement step | Cycle: LAST
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