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- PDB-9vch: Tacrine loaded HFn -

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Basic information

Entry
Database: PDB / ID: 9vch
TitleTacrine loaded HFn
ComponentsFerritin heavy chain
KeywordsMETAL TRANSPORT / Ferritin-drug carrier / Tacrine / Hepatotoxicity / Drug delivery system / Alzheimer's disease
Function / homology
Function and homology information


iron ion sequestering activity / ferritin complex / Scavenging by Class A Receptors / Golgi Associated Vesicle Biogenesis / ferroxidase / negative regulation of ferroptosis / autolysosome / ferroxidase activity / negative regulation of fibroblast proliferation / ferric iron binding ...iron ion sequestering activity / ferritin complex / Scavenging by Class A Receptors / Golgi Associated Vesicle Biogenesis / ferroxidase / negative regulation of ferroptosis / autolysosome / ferroxidase activity / negative regulation of fibroblast proliferation / ferric iron binding / autophagosome / iron ion transport / ferrous iron binding / Iron uptake and transport / 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 / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily
Similarity search - Domain/homology
: / OXYGEN MOLECULE / Ferritin heavy chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsChen, X. / Fan, K.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2021YFC2102900 China
CitationJournal: To Be Published
Title: Spatially Reprogrammed Intrahepatic Trafficking of Ferritin Nanocarriers Mitigates Tacrine-Induced Hepatotoxicity for Alzheimer's Disease Therapy
Authors: Zhao, H. / Chen, X.
History
DepositionJun 6, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 17, 2026Provider: repository / Type: Initial release

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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)21,98121
Polymers21,2561
Non-polymers72520
Water5,314295
1
A: Ferritin heavy chain
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)527,536504
Polymers510,13624
Non-polymers17,400480
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 area103310 Å2
ΔGint-849 kcal/mol
Surface area148840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.565, 183.565, 183.565
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number209
Space group name H-MF432
Space group name HallF423
Components on special symmetry positions
IDModelComponents
11A-205-

CL

21A-207-

CL

31A-215-

MG

41A-216-

MG

51A-422-

HOH

61A-589-

HOH

71A-595-

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: 21255.656 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 / Plasmid: pET30a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P02794, ferroxidase

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Non-polymers , 6 types, 315 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 295 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationN

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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: 3.04 Å3/Da / Density % sol: 59.5 % / Description: Diamond
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 1.5 - 2.0 M MgCl2 and 0.1 M bicine pH 9.0 / PH range: 7.5-9

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: nitrogen gas at 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97914 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97914 Å / Relative weight: 1
ReflectionResolution: 1.7→37.47 Å / Num. obs: 25638 / % possible obs: 86.2 % / Redundancy: 24.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.018 / Rrim(I) all: 0.089 / Net I/σ(I): 25.5
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 25.5 % / Rmerge(I) obs: 0.607 / Mean I/σ(I) obs: 6.6 / Num. unique obs: 3615 / CC1/2: 0.966 / Rpim(I) all: 0.123 / Rrim(I) all: 0.628 / % possible all: 85.5

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→35.33 Å / SU ML: 0.1376 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.4008
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.1796 1230 4.8 %Random
Rwork0.1425 24388 --
obs0.1442 25618 86.26 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.52 Å2
Refinement stepCycle: LAST / Resolution: 1.7→35.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1419 0 26 295 1740
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01391646
X-RAY DIFFRACTIONf_angle_d1.1672230
X-RAY DIFFRACTIONf_chiral_restr0.0751224
X-RAY DIFFRACTIONf_plane_restr0.0143304
X-RAY DIFFRACTIONf_dihedral_angle_d23.4797642
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.770.22011280.1642479X-RAY DIFFRACTION80.94
1.77-1.850.22461690.14773055X-RAY DIFFRACTION99.97
1.85-1.950.2118750.16881518X-RAY DIFFRACTION49.33
1.96-2.070.17311400.1442711X-RAY DIFFRACTION98.31
2.07-2.230.17871650.14473088X-RAY DIFFRACTION99.91
2.23-2.450.1851210.14832706X-RAY DIFFRACTION86.35
2.45-2.810.18791360.14552605X-RAY DIFFRACTION83.09
2.81-3.530.17791610.12833197X-RAY DIFFRACTION99.97
3.54-35.330.16091350.14353029X-RAY DIFFRACTION88.5

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