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- PDB-2nsu: Crystal structure of the ectodomain of human transferrin receptor... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2nsu | ||||||
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Title | Crystal structure of the ectodomain of human transferrin receptor fitted into a cryo-EM reconstruction of canine parvovirus and feline transferrin receptor complex | ||||||
![]() | Transferrin receptor protein 1 | ||||||
![]() | METAL TRANSPORT / transferrin receptor / virus-receptor complex | ||||||
Function / homology | ![]() transferrin receptor activity / negative regulation of mitochondrial fusion / transferrin transport / Transferrin endocytosis and recycling / positive regulation of isotype switching / response to copper ion / response to iron ion / response to manganese ion / RND1 GTPase cycle / RND2 GTPase cycle ...transferrin receptor activity / negative regulation of mitochondrial fusion / transferrin transport / Transferrin endocytosis and recycling / positive regulation of isotype switching / 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 / 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 B cell proliferation / Hsp70 protein binding / RAC1 GTPase cycle / response to nutrient / osteoclast differentiation / cellular response to leukemia inhibitory factor / acute-phase response / clathrin-coated endocytic vesicle membrane / positive regulation of protein-containing complex assembly / HFE-transferrin receptor complex / receptor internalization / recycling endosome / 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 / 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 / early endosome / blood microparticle / endosome membrane / response to hypoxia / intracellular signal transduction / endosome / positive regulation of protein phosphorylation / 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 / cell surface / protein homodimerization activity / RNA binding / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 27 Å | ||||||
![]() | Hafenstein, S. / Kostyuchenko, V.A. / Rossmann, M.G. | ||||||
![]() | ![]() Title: Asymmetric binding of transferrin receptor to parvovirus capsids. Authors: Susan Hafenstein / Laura M Palermo / Victor A Kostyuchenko / Chuan Xiao / Marc C Morais / Christian D S Nelson / Valorie D Bowman / Anthony J Battisti / Paul R Chipman / Colin R Parrish / Michael G Rossmann / ![]() Abstract: Although many viruses are icosahedral when they initially bind to one or more receptor molecules on the cell surface, such an interaction is asymmetric, probably causing a breakdown in the symmetry ...Although many viruses are icosahedral when they initially bind to one or more receptor molecules on the cell surface, such an interaction is asymmetric, probably causing a breakdown in the symmetry and conformation of the original infecting virion in preparation for membrane penetration and release of the viral genome. Cryoelectron microscopy and biochemical analyses show that transferrin receptor, the cellular receptor for canine parvovirus, can bind to only one or a few of the 60 icosahedrally equivalent sites on the virion, indicating that either canine parvovirus has inherent asymmetry or binding of receptor induces asymmetry. The asymmetry of receptor binding to canine parvovirus is reminiscent of the special portal in tailed bacteriophages and some large, icosahedral viruses. Asymmetric interactions of icosahedral viruses with their hosts might be a more common phenomenon than previously thought and may have been obscured by averaging in previous crystallographic and electron microscopic structure determinations. | ||||||
History |
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Remark 999 | SEQUENCE AUTHORS STATE THAT PDB ENTRY 1CX8 WAS USED FOR FITTING IN THIS ENTRY. THE SEQUENCE ... SEQUENCE AUTHORS STATE THAT PDB ENTRY 1CX8 WAS USED FOR FITTING IN THIS ENTRY. THE SEQUENCE DIFFERENCES EXIST IN THE STRUCTURE 1CX8. THE UNIPROT ENTRY P02786 IS A RESULT OF DNA SEQUENCING, WHILE 1CX8 SEQUENCE IS APPARENTLY BASED ON MRNA SEQUENCE. |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 252.8 KB | Display | ![]() |
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PDB format | ![]() | 203 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 740.4 KB | Display | ![]() |
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Full document | ![]() | 827.5 KB | Display | |
Data in XML | ![]() | 49 KB | Display | |
Data in CIF | ![]() | 72.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1288MC ![]() 1287C M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 71622.961 Da / Num. of mol.: 2 / Fragment: THE ECTODOMAIN OF HUMAN TRANSFERRIN RECEPTOR Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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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: MIXTURE OF EMPTY CANINE PARVOVIRUS CAPSIDS AND ECTODOMAINS OF FELINE TRANSFERRIN RECEPTORS Type: VIRUS / Details: Based on PDB entry 1CX8 |
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Buffer solution | Name: 0.02M TRIS-HCL / pH: 7.5 / Details: 0.02M TRIS-HCL |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: QUANTIFOIL 200 |
Vitrification | Cryogen name: ETHANE / Details: PLUNGED IN LIQUID ETHANE |
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Electron microscopy imaging
Microscopy | Model: FEI/PHILIPS CM200FEG / Date: Jan 22, 2003 |
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Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 50000 X / Calibrated magnification: 54000 X / Nominal defocus max: 3900 nm / Nominal defocus min: 1700 nm / Cs: 2 mm |
Image recording | Electron dose: 25.96 e/Å2 / Film or detector model: KODAK SO-163 FILM |
Image scans | Num. digital images: 115 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
Radiation wavelength | Relative weight: 1 |
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Processing
EM software |
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CTF correction | Details: CTF correction of each particle | ||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||
3D reconstruction | Method: projection matching / Resolution: 27 Å / Num. of particles: 8566 / Nominal pixel size: 2.6 Å / Actual pixel size: 2.6 Å / Details: a modified version of XMIPP software was used / Symmetry type: POINT | ||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL / Target criteria: BEST VISUAL FIT USING THE PROGRAM O Details: METHOD--MANUAL FITTING USING THE PROGRAM O REFINEMENT PROTOCOL--RIGID BODY | ||||||||||||
Atomic model building | PDB-ID: 1CX8 Accession code: 1CX8 / Source name: PDB / Type: experimental model | ||||||||||||
Refinement | Highest resolution: 27 Å | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 27 Å
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