+Open data
-Basic information
Entry | Database: PDB / ID: 1a8e | ||||||
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Title | HUMAN SERUM TRANSFERRIN, RECOMBINANT N-TERMINAL LOBE | ||||||
Components | SERUM TRANSFERRIN | ||||||
Keywords | IRON TRANSPORT / GLYCOPROTEIN / TRANSFERRIN / NLOBE / 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 / positive regulation of bone resorption / positive regulation of phosphorylation / endocytic vesicle / basal plasma membrane / clathrin-coated pit ...iron chaperone activity / Transferrin endocytosis and recycling / transferrin receptor binding / basal part of cell / positive regulation of cell motility / positive regulation of bone resorption / positive regulation of phosphorylation / endocytic vesicle / basal plasma membrane / clathrin-coated pit / ERK1 and ERK2 cascade / ferric iron binding / osteoclast differentiation / clathrin-coated endocytic vesicle membrane / actin filament organization / cellular response to iron ion / Post-translational protein phosphorylation / Iron uptake and transport / 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) / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / late endosome / Platelet degranulation / iron ion transport / antibacterial humoral response / cytoplasmic vesicle / secretory granule lumen / intracellular iron ion homeostasis / vesicle / blood microparticle / endosome membrane / early endosome / apical plasma membrane / endoplasmic reticulum lumen / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / cell surface / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Macgillivray, R.T.A. / Moore, S.A. / Chen, J. / Anderson, B.F. / Baker, H. / Luo, Y. / Bewley, M. / Smith, C.A. / Murphy, M.E.P. / Wang, Y. ...Macgillivray, R.T.A. / Moore, S.A. / Chen, J. / Anderson, B.F. / Baker, H. / Luo, Y. / Bewley, M. / Smith, C.A. / Murphy, M.E.P. / Wang, Y. / Mason, A.B. / Woodworth, R.C. / Brayer, G.D. / Baker, E.N. | ||||||
Citation | Journal: Biochemistry / Year: 1998 Title: Two high-resolution crystal structures of the recombinant N-lobe of human transferrin reveal a structural change implicated in iron release. Authors: MacGillivray, R.T. / Moore, S.A. / Chen, J. / Anderson, B.F. / Baker, H. / Luo, Y. / Bewley, M. / Smith, C.A. / Murphy, M.E. / Wang, Y. / Mason, A.B. / Woodworth, R.C. / Brayer, G.D. / Baker, E.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1a8e.cif.gz | 79.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1a8e.ent.gz | 59.4 KB | Display | PDB format |
PDBx/mmJSON format | 1a8e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1a8e_validation.pdf.gz | 428.3 KB | Display | wwPDB validaton report |
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Full document | 1a8e_full_validation.pdf.gz | 429.6 KB | Display | |
Data in XML | 1a8e_validation.xml.gz | 15.1 KB | Display | |
Data in CIF | 1a8e_validation.cif.gz | 21.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a8/1a8e ftp://data.pdbj.org/pub/pdb/validation_reports/a8/1a8e | HTTPS FTP |
-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: 36408.414 Da / Num. of mol.: 1 / Fragment: N-TERMINAL LOBE Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line: BABY HAMSTER KIDNEY CELLS / Cellular location: EXTRACELLULAR / Organ: 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: 2.4 Å3/Da / Density % sol: 50 % | ||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.75 Details: PROTEIN WAS CRYSTALLIZED FROM 26% PEG 4000. BUFFER WAS 40MM NA CACODYLATE, PH 5.75, WITH 20MM NA BICARBONATE. CRYSTALS GROWN AT 4 DEGREES C USING THE HANGING DROP METHOD., vapor diffusion - ...Details: PROTEIN WAS CRYSTALLIZED FROM 26% PEG 4000. BUFFER WAS 40MM NA CACODYLATE, PH 5.75, WITH 20MM NA BICARBONATE. CRYSTALS GROWN AT 4 DEGREES C USING THE HANGING DROP METHOD., vapor diffusion - hanging drop, temperature 277K | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: May 1, 1990 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→30 Å / Num. obs: 39418 / % possible obs: 82.4 % / Observed criterion σ(I): 3 / Redundancy: 1.8 % / Biso Wilson estimate: 35 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 14.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: RABBIT TRANSFERRIN Resolution: 1.6→30 Å / Isotropic thermal model: BCORREL (MODIFIED) / σ(F): 0 / Stereochemistry target values: PROTGEO_EH (MODIFIED)
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Solvent computation | Solvent model: BABINET / Bsol: 160 Å2 / ksol: 0.86 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→30 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Version: 5EA / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.181 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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