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Yorodumi- PDB-2nsu: Crystal structure of the ectodomain of human transferrin receptor... -
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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 | ||||||
Components | Transferrin receptor protein 1 | ||||||
Keywords | METAL TRANSPORT / transferrin receptor / virus-receptor complex | ||||||
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 / Differentiation of keratinocytes in interfollicular epidermis in mammalian skin / response to copper ion / response to iron ion / RND1 GTPase cycle / response to manganese ion ...transferrin receptor activity / negative regulation of mitochondrial fusion / transferrin transport / Transferrin endocytosis and recycling / positive regulation of isotype switching / 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 / positive regulation of bone resorption / RHOB GTPase cycle / Golgi Associated Vesicle Biogenesis / RHOC GTPase cycle / RHOJ GTPase cycle / RHOQ GTPase cycle / CDC42 GTPase cycle / RHOH GTPase cycle / RHOG GTPase cycle / transport across blood-brain barrier / RHOA GTPase cycle / RAC2 GTPase cycle / RAC3 GTPase cycle / response to nutrient / 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 / osteoclast differentiation / clathrin-coated endocytic vesicle membrane / cellular response to leukemia inhibitory factor / acute-phase response / 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 / 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 / blood microparticle / endosome / endosome membrane / early endosome / response to hypoxia / intracellular signal transduction / positive regulation of protein phosphorylation / external side of plasma membrane / intracellular membrane-bounded organelle / 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 / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 27 Å | ||||||
Authors | Hafenstein, S. / Kostyuchenko, V.A. / Rossmann, M.G. | ||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2007 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. |
-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 2nsu.cif.gz | 252.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2nsu.ent.gz | 203 KB | Display | PDB format |
PDBx/mmJSON format | 2nsu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2nsu_validation.pdf.gz | 740.4 KB | Display | wwPDB validaton report |
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Full document | 2nsu_full_validation.pdf.gz | 827.5 KB | Display | |
Data in XML | 2nsu_validation.xml.gz | 49 KB | Display | |
Data in CIF | 2nsu_validation.cif.gz | 72.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ns/2nsu ftp://data.pdbj.org/pub/pdb/validation_reports/ns/2nsu | HTTPS FTP |
-Related structure data
Related structure data | 1288MC 1287C 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: 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.) Homo sapiens (human) / Gene: TFRC / Plasmid: PCMVTFR / Organ (production host): OVARY CELLS / Production host: Cricetulus griseus (Chinese hamster) / 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
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 |
-Electron microscopy imaging
Microscopy | Model: FEI/PHILIPS CM200FEG / Date: Jan 22, 2003 |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
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 |
-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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