+Open data
-Basic information
Entry | Database: PDB / ID: 1d4n | ||||||
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Title | HUMAN SERUM TRANSFERRIN | ||||||
Components | TRANSFERRIN | ||||||
Keywords | METAL TRANSPORT / IRON TRANSPORT / GLYCOPROTEIN / TRANSFERRIN / N-LOBE / IRON-RELEASE / CARBONATE | ||||||
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 / clathrin-coated pit / positive regulation of phosphorylation / 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 / clathrin-coated pit / positive regulation of phosphorylation / ERK1 and ERK2 cascade / ferric iron binding / osteoclast differentiation / basal plasma membrane / actin filament organization / cellular response to iron ion / Post-translational protein phosphorylation / Iron uptake and transport / clathrin-coated endocytic vesicle membrane / ferrous iron binding / regulation of protein stability / regulation of iron ion transport / HFE-transferrin receptor complex / 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 / iron ion transport / antibacterial humoral response / cytoplasmic vesicle / secretory granule lumen / intracellular iron ion homeostasis / vesicle / blood microparticle / 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 / Resolution: 2 Å | ||||||
Authors | Yang, H.-W. / MacGillivray, R.T.A. / Chen, J. / Luo, Y. / Wang, Y. / Brayer, G.D. / Mason, A. / Woodworth, R.C. / Murphy, M.E.P. | ||||||
Citation | Journal: Protein Sci. / Year: 2000 Title: Crystal structures of two mutants (K206Q, H207E) of the N-lobe of human transferrin with increased affinity for iron. Authors: Yang, A.H. / MacGillivray, R.T. / Chen, J. / Luo, Y. / Wang, Y. / Brayer, G.D. / Mason, A.B. / Woodworth, R.C. / Murphy, M.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1d4n.cif.gz | 74.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1d4n.ent.gz | 59.3 KB | Display | PDB format |
PDBx/mmJSON format | 1d4n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d4/1d4n ftp://data.pdbj.org/pub/pdb/validation_reports/d4/1d4n | HTTPS FTP |
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-Related 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: 36399.379 Da / Num. of mol.: 1 / Fragment: N-TERMINAL LOBE / Mutation: H207E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Tissue: BLOOD / Plasmid: PNUT-BHK / Organ (production host): KIDNEY / Production host: Cricetinae (hamsters) / 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: 2.43 Å3/Da / Density % sol: 49.44 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.75 Details: PEG 4000, SODIUM BICARBONATE, SODIUM CACODYLATE, pH 5.75, VAPOR DIFFUSION, HANGING DROP, temperature 277K | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃Details: drop solution was mixed with an equal volume of reservoir solution | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→32 Å / Num. obs: 21745 / % possible obs: 88 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 20.8 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 20.1 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.13 / % possible all: 89 |
Reflection shell | *PLUS % possible obs: 89 % / Mean I/σ(I) obs: 7.9 |
-Processing
Software |
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Refinement | Resolution: 2→32 Å / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 2→32 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.26 / Rfactor Rwork: 0.249 |