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- PDB-7ck9: Crystal structure of Doxorubicin loaded human ferritin heavy chain -

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Basic information

Entry
Database: PDB / ID: 7ck9
TitleCrystal structure of Doxorubicin loaded human ferritin heavy chain
ComponentsFerritin heavy chain
KeywordsMETAL TRANSPORT / iron storage / ferroxidase activity / nancage
Function / homology
Function and homology information


iron ion sequestering activity / ferritin complex / Scavenging by Class A Receptors / negative regulation of ferroptosis / Golgi Associated Vesicle Biogenesis / ferroxidase / autolysosome / ferroxidase activity / negative regulation of fibroblast proliferation / ferric iron binding ...iron ion sequestering activity / ferritin complex / Scavenging by Class A Receptors / negative regulation of ferroptosis / Golgi Associated Vesicle Biogenesis / ferroxidase / autolysosome / ferroxidase activity / negative regulation of fibroblast proliferation / ferric iron binding / autophagosome / iron ion transport / Iron uptake and transport / ferrous iron binding / tertiary granule lumen / ficolin-1-rich granule lumen / intracellular iron ion homeostasis / immune response / iron ion binding / negative regulation of cell population proliferation / Neutrophil degranulation / extracellular exosome / extracellular region / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Ferritin iron-binding regions signature 1. / Ferritin iron-binding regions signature 2. / Ferritin, conserved site / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain ...Ferritin iron-binding regions signature 1. / Ferritin iron-binding regions signature 2. / Ferritin, conserved site / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
OXYGEN MOLECULE / Ferritin heavy chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.602 Å
AuthorsChen, X. / Jiang, B. / Yan, X. / Fan, K.
Funding support China, 4items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31530026 China
National Natural Science Foundation of China (NSFC)31871005 China
National Natural Science Foundation of China (NSFC)31770793 China
National Natural Science Foundation of China (NSFC)31900981 China
CitationJournal: 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
DepositionJul 16, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ferritin heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,45510
Polymers20,1171
Non-polymers3399
Water5,350297
1
A: Ferritin heavy chain
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)490,929240
Polymers482,79724
Non-polymers8,132216
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation11_555y,-z,-x1
crystal symmetry operation12_555-y,-z,x1
crystal symmetry operation13_555y,x,-z1
crystal symmetry operation14_555-y,-x,-z1
crystal symmetry operation15_555y,-x,z1
crystal symmetry operation16_555-y,x,z1
crystal symmetry operation17_555x,z,-y1
crystal symmetry operation18_555-x,z,y1
crystal symmetry operation19_555-x,-z,-y1
crystal symmetry operation20_555x,-z,y1
crystal symmetry operation21_555z,y,-x1
crystal symmetry operation22_555z,-y,x1
crystal symmetry operation23_555-z,y,x1
crystal symmetry operation24_555-z,-y,-x1
Buried area103110 Å2
ΔGint-557 kcal/mol
Surface area138700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.207, 183.207, 183.207
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number209
Space group name H-MF432
Components on special symmetry positions
IDModelComponents
11A-201-

CL

21A-205-

MG

31A-206-

MG

41A-332-

HOH

51A-570-

HOH

61A-588-

HOH

71A-597-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Ferritin heavy chain / Ferritin H subunit / Cell proliferation-inducing gene 15 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 / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.05 Å3/Da / Density % sol: 59.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Bicine, pH 9.0, 1.7 - 2 M MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97905 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 7, 2018
RadiationMonochromator: DCM with Si(111) crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97905 Å / Relative weight: 1
ReflectionResolution: 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

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2
1.6-1.6625.50.30211.4634450.9870.9970.0610.3080.614
1.66-1.7225.30.24314.6334380.9920.9980.0490.2480.698
1.72-1.824.20.19119.9234420.9940.9980.0390.1960.874
1.8-1.924.80.15726.1534430.9950.9990.0320.161.073
1.9-2.0225.70.12832.2834720.9980.9990.0260.130.963
2.02-2.1724.10.10637.5434770.9970.9990.0220.1091.071
2.17-2.3925.50.09238.0835100.99810.0190.0940.91
2.39-2.7425.40.08146.5135170.99810.0160.0831.084
2.74-3.4525.20.06749.835790.99910.0140.0680.992
3.45-3023.50.0647.6438120.9970.9990.0130.0621.002

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5N27

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
RfactorNum. reflection% reflection
Rfree0.1685 1803 5.13 %
Rwork0.1492 33330 -
obs0.1502 35133 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.33 Å2 / Biso mean: 22.3964 Å2 / Biso min: 11.16 Å2
Refinement stepCycle: final / Resolution: 1.602→27.939 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1413 0 15 297 1725
Biso mean--40.72 36.04 -
Num. residues----172
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.602-1.64520.15571370.13192509
1.6452-1.69360.1811320.13782481
1.6936-1.74830.1521390.14732529
1.7483-1.81080.17871130.14742547
1.8108-1.88320.17871560.15152512
1.8832-1.96890.18111510.15362515
1.9689-2.07270.15921200.14392517
2.0727-2.20250.14941460.13872559
2.2025-2.37250.15681400.14582538
2.3725-2.61110.15761330.15642583
2.6111-2.98850.181180.15772613
2.9885-3.76380.15071660.14372618
3.7638-27.9390.19461520.1542809

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