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Yorodumi- PDB-7ck9: Crystal structure of Doxorubicin loaded human ferritin heavy chain -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ck9 | |||||||||||||||
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Title | Crystal structure of Doxorubicin loaded human ferritin heavy chain | |||||||||||||||
Components | Ferritin heavy chain | |||||||||||||||
Keywords | METAL TRANSPORT / iron storage / ferroxidase activity / nancage | |||||||||||||||
Function / homology | Function and homology information iron ion sequestering activity / : / autolysosome / Scavenging by Class A Receptors / Golgi Associated Vesicle Biogenesis / ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / negative regulation of fibroblast proliferation / ferric iron binding ...iron ion sequestering activity / : / autolysosome / Scavenging by Class A Receptors / Golgi Associated Vesicle Biogenesis / ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / negative regulation of fibroblast proliferation / ferric iron binding / ferrous iron binding / Iron uptake and transport / tertiary granule lumen / iron ion transport / intracellular iron ion homeostasis / ficolin-1-rich granule lumen / immune response / iron ion binding / negative regulation of cell population proliferation / Neutrophil degranulation / extracellular exosome / extracellular region / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.602 Å | |||||||||||||||
Authors | Chen, X. / Jiang, B. / Yan, X. / Fan, K. | |||||||||||||||
Funding support | China, 4items
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Citation | Journal: Nano Today / Year: 2020 Title: A natural drug entry channel in the ferritin nanocage. Authors: Jiang, B. / Chen, X. / Sun, G. / Chen, X. / Yin, Y. / Jin, Y. / Mi, Q. / Ma, L. / Yang, Y. / Yan, X. / Fan, K. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ck9.cif.gz | 63.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ck9.ent.gz | 45.8 KB | Display | PDB format |
PDBx/mmJSON format | 7ck9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ck/7ck9 ftp://data.pdbj.org/pub/pdb/validation_reports/ck/7ck9 | HTTPS FTP |
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-Related structure data
Related structure data | 7ck8C 5n27S S: Starting model for refinement 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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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 20116.547 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FTH1, FTH, FTHL6, OK/SW-cl.84, PIG15 / Production host: Escherichia coli (E. coli) / References: UniProt: P02794, ferroxidase |
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-Non-polymers , 5 types, 306 molecules
#2: Chemical | ChemComp-CL / #3: Chemical | #4: Chemical | ChemComp-OXY / | #5: Chemical | ChemComp-GOL / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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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: 3.05 Å3/Da / Density % sol: 59.7 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Bicine, pH 9.0, 1.7 - 2 M MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97905 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 7, 2018 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: DCM with Si(111) crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97905 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.6→30 Å / Num. obs: 35135 / % possible obs: 100 % / Redundancy: 24.9 % / Biso Wilson estimate: 18.22 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.016 / Rrim(I) all: 0.078 / Χ2: 0.928 / Net I/av σ(I): 11.46 / Net I/σ(I): 11.9 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / % possible all: 100
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5N27 Resolution: 1.602→27.939 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 14.61 / Stereochemistry target values: ML Details: XYZ cordinates, Individual B factors and occupancies refinement
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 91.33 Å2 / Biso mean: 22.3964 Å2 / Biso min: 11.16 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.602→27.939 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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