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- PDB-5yi5: human ferritin mutant - E-helix deletion -

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Basic information

Entry
Database: PDB / ID: 5yi5
Titlehuman ferritin mutant - E-helix deletion
ComponentsFerritin heavy chain
KeywordsTRANSPORT PROTEIN / ferritin / cage / drug delivery
Function/homologyautolysosome / Scavenging by Class A Receptors / intracellular ferritin complex / Ferritin iron-binding regions signature 1. / Ferritin iron-binding regions signature 2. / Ferritin, conserved site / Golgi Associated Vesicle Biogenesis / ferroxidase / intracellular sequestering of iron ion / Ferritin ...autolysosome / Scavenging by Class A Receptors / intracellular ferritin complex / Ferritin iron-binding regions signature 1. / Ferritin iron-binding regions signature 2. / Ferritin, conserved site / Golgi Associated Vesicle Biogenesis / ferroxidase / intracellular sequestering of iron ion / Ferritin / ferroxidase activity / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / negative regulation of fibroblast proliferation / Ferritin/DPS protein domain / Ferritin-like / iron ion transport / ferric iron binding / Iron uptake and transport / Ferritin-like superfamily / Ferritin-like domain / cellular iron ion homeostasis / tertiary granule lumen / ficolin-1-rich granule lumen / immune response / negative regulation of cell proliferation / iron ion binding / Neutrophil degranulation / neutrophil degranulation / extracellular exosome / extracellular region / nucleus / cytosol / Ferritin heavy chain
Function and homology information
Specimen sourceHomo sapiens / human /
MethodElectron microscopy (3 Å resolution / Particle / Single particle) / Transmission electron microscopy
AuthorsLee, S.G. / Yoon, H.R. / Ahn, B.J. / Jeong, H. / Hyun, J. / Jung, Y. / Kim, H.
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2018
Title: Four-fold Channel-Nicked Human Ferritin Nanocages for Active Drug Loading and pH-Responsive Drug Release.
Authors: Byungjun Ahn / Seong-Gyu Lee / Hye Ryeon Yoon / Jeong Min Lee / Hyeok Jin Oh / Ho Min Kim / Yongwon Jung
Abstract: Human ferritins are emerging platforms for non-toxic protein-based drug delivery, owing to their intrinsic or acquirable targeting abilities to cancer cells and hollow cage structures for drug ...Human ferritins are emerging platforms for non-toxic protein-based drug delivery, owing to their intrinsic or acquirable targeting abilities to cancer cells and hollow cage structures for drug loading. However, reliable strategies for high-level drug encapsulation within ferritin cavities and prompt cellular drug release are still lacking. Ferritin nanocages were developed with partially opened hydrophobic channels, which provide stable routes for spontaneous and highly accumulated loading of Fe -conjugated drugs as well as pH-responsive rapid drug release at endoplasmic pH. Multiple cancer-related compounds, such as doxorubicin, curcumin, and quercetin, were actively and heavily loaded onto the prepared nicked ferritin. Drugs on these minimally modified ferritins were effectively delivered inside cancer cells with high toxicity.
Copyright: 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Oct 2, 2017 / Release: Feb 21, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Feb 21, 2018Structure modelrepositoryInitial release
1.1Mar 14, 2018Structure modelDatabase referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

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Assembly

Deposited unit
A: Ferritin heavy chain
B: Ferritin heavy chain
C: Ferritin heavy chain
D: Ferritin heavy chain
E: Ferritin heavy chain
F: Ferritin heavy chain
G: Ferritin heavy chain
H: Ferritin heavy chain
I: Ferritin heavy chain
J: Ferritin heavy chain
K: Ferritin heavy chain
L: Ferritin heavy chain
M: Ferritin heavy chain
N: Ferritin heavy chain
O: Ferritin heavy chain
P: Ferritin heavy chain
Q: Ferritin heavy chain
R: Ferritin heavy chain
S: Ferritin heavy chain
T: Ferritin heavy chain
U: Ferritin heavy chain
V: Ferritin heavy chain
W: Ferritin heavy chain
X: Ferritin heavy chain


Theoretical massNumber of molelcules
Total (without water)494,59524
Polyers494,59524
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)88190
ΔGint (kcal/M)-337
Surface area (Å2)162770

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Components

#1: Protein/peptide ...
Ferritin heavy chain / Ferritin H subunit / Cell proliferation-inducing gene 15 protein


Mass: 20608.105 Da / Num. of mol.: 24 / Source: (gene. exp.) Homo sapiens / human / / Gene: FTH1, FTH, FTHL6, OK/SW-cl.84, PIG15 / Production host: Escherichia coli / References: UniProt:P02794, EC:1.16.3.1 (ferroxidase)

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: human ferritin E-helix deletion mutant / Type: COMPLEX / Entity ID: 1 / Source: RECOMBINANT
Molecular weightValue: 0.42 deg. / Units: MEGADALTONS / Experimental value: NO
Source (natural)Organism: Homo sapiens
Source (recombinant)Organism: Escherichia coli
Buffer solutionDetails: buffers were titrated with HCl to pH7.2 / pH: 7.2
Buffer component
IDConc.UnitsNameFormulaBuffer ID
1150mMsodium chlorideNaCl1
250mMtris(hydroxymethyl)aminomethaneTris1
SpecimenConc.: 0.05 mg/ml / Details: this sample was monodisperse / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: the grid was coated with graphene oxide prior to use
Grid material: COPPER / Grid mesh size: 400 / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 276 kelvins / Details: blot for 9 seconds before plunging

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 47000 / Cs: 0.002 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1.8 sec. / Electron dose: 2 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)
Image scansMovie frames/image: 30 / Used frames/image: 2-29

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Processing

EM software
IDNameVersionCategory
2RELION2.0IMAGE ACQUISITION
4CTFFIND4.0CTF CORRECTION
7UCSF Chimera1.10.2MODEL FITTING
9RELION2.0INITIAL EULER ASSIGNMENT
10RELION2.0FINAL EULER ASSIGNMENT
11RELION2.0CLASSIFICATION
12RELION2.0RECONSTRUCTION
13PHENIX1.10.1MODEL REFINEMENT
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNumber of particles selected: 623510
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 429135 / Details: relion2.0 program was used for the reconstruction / Symmetry type: POINT
Atomic model buildingOverall b value: 29.56 / Ref protocol: FLEXIBLE FIT / Ref space: REAL
Atomic model buildingPDB-ID: 4Y08
Pdb chain ID: A / Pdb chain residue range: 5-160

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