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Yorodumi- PDB-3fgs: Crystal structure of G65R/K206E double mutant of the N-lobe human... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3fgs | ||||||
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Title | Crystal structure of G65R/K206E double mutant of the N-lobe human transferrin | ||||||
Components | Serotransferrin | ||||||
Keywords | METAL TRANSPORT / Human transferrin / Iron binding protein / Dilysine pair / Disease mutation / Glycoprotein / Ion transport / Iron / Iron transport / Metal-binding / Methylation / Phosphoprotein / Polymorphism / Secreted / Transport | ||||||
Function / homology | Function and homology information iron chaperone activity / Transferrin endocytosis and recycling / transferrin receptor binding / basal part of cell / positive regulation of cell motility / endocytic vesicle / positive regulation of bone resorption / positive regulation of phosphorylation / clathrin-coated pit / ERK1 and ERK2 cascade ...iron chaperone activity / Transferrin endocytosis and recycling / transferrin receptor binding / basal part of cell / positive regulation of cell motility / endocytic vesicle / positive regulation of bone resorption / positive regulation of phosphorylation / clathrin-coated pit / ERK1 and ERK2 cascade / osteoclast differentiation / basal plasma membrane / ferric iron binding / actin filament organization / ferrous iron binding / Post-translational protein phosphorylation / Iron uptake and transport / clathrin-coated endocytic vesicle membrane / regulation of protein stability / regulation of iron ion transport / HFE-transferrin receptor complex / cellular response to iron ion / recycling endosome / positive regulation of receptor-mediated endocytosis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / late endosome / Cargo recognition for clathrin-mediated endocytosis / Platelet degranulation / Clathrin-mediated endocytosis / antibacterial humoral response / iron ion transport / cytoplasmic vesicle / secretory granule lumen / blood microparticle / vesicle / intracellular iron ion homeostasis / early endosome / endosome membrane / apical plasma membrane / endoplasmic reticulum lumen / perinuclear region of cytoplasm / positive regulation of DNA-templated transcription / cell surface / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å | ||||||
Authors | Halbrooks, P.J. / Mason, A.B. / Everse, S.J. | ||||||
Citation | Journal: Biochemistry / Year: 2009 Title: Structural and Functional Consequences of the Substitution of Glycine 65 with Arginine in the N-Lobe of Human Transferrin. Authors: Mason, A.B. / Halbrooks, P.J. / James, N.G. / Byrne, S.L. / Grady, J.K. / Chasteen, N.D. / Bobst, C.E. / Kaltashov, I.A. / Smith, V.C. / Macgillivray, R.T. / Everse, S.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3fgs.cif.gz | 80.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fgs.ent.gz | 63.1 KB | Display | PDB format |
PDBx/mmJSON format | 3fgs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fg/3fgs ftp://data.pdbj.org/pub/pdb/validation_reports/fg/3fgs | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 37315.344 Da / Num. of mol.: 1 / Fragment: Peptidase S60 1 domain / Mutation: G65R, K206E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PRO1400, TF, transferrin / Plasmid: pNUT / Production host: Mesocricetus auratus (golden hamster) / Strain (production host): BHK / References: UniProt: P02787 |
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#2: Chemical | ChemComp-CO3 / |
#3: Chemical | ChemComp-FE / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.49 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.7 Details: 200 mM potassium acetate buffer (pH 7.7) containing 10 mM KCl and 18% polyethylene glycol 3350. Concentration of the mutant was 17.5 mg/mL. Crystals appeared in approximately a week ...Details: 200 mM potassium acetate buffer (pH 7.7) containing 10 mM KCl and 18% polyethylene glycol 3350. Concentration of the mutant was 17.5 mg/mL. Crystals appeared in approximately a week following micro-seeding with wild-type N-lobe, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 7, 2001 / Details: Xenocs FOX-2D Multilayer Mirrors | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→30 Å / Num. obs: 29637 / % possible obs: 93.3 % / Rmerge(I) obs: 0.049 / Χ2: 1.511 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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Phasing MR | Method rotation: fast direct / Method translation: &STRIP%trans_method |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→19.49 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0
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Solvent computation | Bsol: 36.137 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso max: 45.94 Å2 / Biso mean: 14.999 Å2 / Biso min: 5.79 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→19.49 Å
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Refine LS restraints |
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Xplor file |
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