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Yorodumi- PDB-1cx8: CRYSTAL STRUCTURE OF THE ECTODOMAIN OF HUMAN TRANSFERRIN RECEPTOR -
+Open data
-Basic information
Entry | Database: PDB / ID: 1cx8 | ||||||
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Title | CRYSTAL STRUCTURE OF THE ECTODOMAIN OF HUMAN TRANSFERRIN RECEPTOR | ||||||
Components | TRANSFERRIN RECEPTOR PROTEIN | ||||||
Keywords | METAL TRANSPORT / HUMAN TRANSFERRIN RECEPTOR | ||||||
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 | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.2 Å | ||||||
Authors | Lawrence, C.M. / Ray, S. / Babyonyshev, M. / Galluser, R. / Borhani, D. / Harrison, S.C. | ||||||
Citation | Journal: Science / Year: 1999 Title: Crystal structure of the ectodomain of human transferrin receptor. Authors: Lawrence, C.M. / Ray, S. / Babyonyshev, M. / Galluser, R. / Borhani, D.W. / Harrison, S.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1cx8.cif.gz | 968.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1cx8.ent.gz | 810.1 KB | Display | PDB format |
PDBx/mmJSON format | 1cx8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1cx8_validation.pdf.gz | 561.6 KB | Display | wwPDB validaton report |
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Full document | 1cx8_full_validation.pdf.gz | 928.7 KB | Display | |
Data in XML | 1cx8_validation.xml.gz | 220.1 KB | Display | |
Data in CIF | 1cx8_validation.cif.gz | 288.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cx/1cx8 ftp://data.pdbj.org/pub/pdb/validation_reports/cx/1cx8 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 71622.961 Da / Num. of mol.: 8 / Fragment: RESIDUES 122-760 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PCMVTFR / Organ (production host): OVARY CELLS / Production host: Cricetinae gen. sp. (mammal) / References: UniProt: P02786 #2: Sugar | ChemComp-NAG / #3: Chemical | ChemComp-SM / |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.61 Å3/Da / Density % sol: 65.91 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.7 Details: 2.4 M KCl 10 mM KPi 1.5% PEG 20K, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 18K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 9, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→15 Å / Num. all: 110528 / Num. obs: 110528 / % possible obs: 82 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 40 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 3.2→3.25 Å / Redundancy: 2 % / Rmerge(I) obs: 0.337 / Num. unique all: 2143 / % possible all: 32 |
Reflection | *PLUS |
-Processing
Software |
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Refinement | Resolution: 3.2→8 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 3.2→8 Å
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Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 3.2 Å / Lowest resolution: 8 Å / σ(F): 0 / Rfactor obs: 0.24 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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