+Open data
-Basic information
Entry | Database: PDB / ID: 1suv | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of Human Transferrin Receptor-Transferrin Complex | ||||||
Components |
| ||||||
Keywords | METAL TRANSPORT / Protein Complex | ||||||
Function / homology | Function and homology information 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 iron 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 iron ion / response to copper 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 / RHOH GTPase cycle / CDC42 GTPase cycle / transport across blood-brain barrier / endocytic vesicle / 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 / clathrin-coated pit / positive regulation of phosphorylation / ERK1 and ERK2 cascade / Hsp70 protein binding / positive regulation of T cell proliferation / RAC1 GTPase cycle / cellular response to leukemia inhibitory factor / basal plasma membrane / ferric iron binding / osteoclast differentiation / response to nutrient / actin filament organization / Post-translational protein phosphorylation / acute-phase response / positive regulation of protein-containing complex assembly / ferrous iron binding / clathrin-coated endocytic vesicle membrane / Iron uptake and transport / regulation of protein stability / regulation of iron ion transport / receptor internalization / HFE-transferrin receptor complex / cellular response to iron ion / 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) / extracellular vesicle / melanosome / cellular response to xenobiotic stimulus / late endosome / double-stranded RNA binding / Cargo recognition for clathrin-mediated endocytosis / Platelet degranulation / virus receptor activity / Clathrin-mediated endocytosis / positive regulation of peptidyl-serine phosphorylation / positive regulation of NF-kappaB transcription factor activity / antibacterial humoral response / iron ion transport / cytoplasmic vesicle / basolateral plasma membrane / blood microparticle / positive regulation of canonical NF-kappaB signal transduction / secretory granule lumen / intracellular iron ion homeostasis / vesicle / response to hypoxia / early endosome / endosome membrane / endosome / intracellular signal transduction / 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 / perinuclear region of cytoplasm / positive regulation of DNA-templated transcription / cell surface / protein homodimerization activity / extracellular space / RNA binding / extracellular exosome / extracellular region Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.5 Å | ||||||
Authors | Cheng, Y. / Zak, O. / Aisen, P. / Harrison, S.C. / Walz, T. | ||||||
Citation | Journal: Cell / Year: 2004 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 |
| ||||||
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. |
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 1suv.cif.gz | 504.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1suv.ent.gz | 422 KB | Display | PDB format |
PDBx/mmJSON format | 1suv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/su/1suv ftp://data.pdbj.org/pub/pdb/validation_reports/su/1suv | HTTPS FTP |
---|
-Related structure data
Related structure data | |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
Symmetry | Point symmetry: (Schoenflies symbol: C2 (2 fold cyclic)) |
-Components
#1: Protein | Mass: 71622.961 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TFRC / Cell (production host): ovary / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P02786 #2: Protein | Mass: 36408.414 Da / Num. of mol.: 2 / Fragment: repeat 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TF / Cell (production host): kidney / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P02787 #3: Protein | Mass: 38300.445 Da / Num. of mol.: 2 / Fragment: repeat 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TF / Cell (production host): kidney / Production host: Cricetulus griseus (Chinese hamster) #4: Chemical | ChemComp-CO3 / #5: Chemical | ChemComp-FE / |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Human Transferrin Receptor - Transferrin Complex / Type: COMPLEX |
---|---|
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TECNAI F20 / Date: Oct 15, 2001 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / 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 |
-Processing
CTF correction | Details: CTF correction for each particle | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 |
| ||||||||||||
Refinement step | Cycle: LAST
|