[English] 日本語
Yorodumi
- PDB-5yi5: human ferritin mutant - E-helix deletion -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 5yi5
Titlehuman ferritin mutant - E-helix deletion
ComponentsFerritin heavy chain
KeywordsTRANSPORT PROTEIN / ferritin / cage / drug delivery
Function / homologyFerritin-like superfamily / Ferritin-like / Ferritin-like diiron domain / Ferritin/DPS protein domain / Ferritin / Ferritin, conserved site / Ferritin-like domain / Ferritin iron-binding regions signature 2. / Ferritin iron-binding regions signature 1. / Ferritin-like diiron domain profile. ...Ferritin-like superfamily / Ferritin-like / Ferritin-like diiron domain / Ferritin/DPS protein domain / Ferritin / Ferritin, conserved site / Ferritin-like domain / Ferritin iron-binding regions signature 2. / Ferritin iron-binding regions signature 1. / Ferritin-like diiron domain profile. / Scavenging by Class A Receptors / Golgi Associated Vesicle Biogenesis / Neutrophil degranulation / Iron uptake and transport / iron ion import / autolysosome / intracellular ferritin complex / ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / negative regulation of fibroblast proliferation / ferric iron binding / cellular iron ion homeostasis / tertiary granule lumen / ficolin-1-rich granule lumen / immune response / iron ion binding / negative regulation of cell proliferation / neutrophil degranulation / extracellular exosome / extracellular region / nucleus / cytosol / Ferritin heavy chain
Function and homology information
Specimen sourceHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3 Å resolution
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.
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

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-6830
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 (E. coli) / References: UniProt: P02794, ferroxidase

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: human ferritin E-helix deletion mutant / Type: COMPLEX / Entity ID: 1 / Source: RECOMBINANT
Molecular weightValue: 0.42 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionDetails: buffers were titrated with HCl to pH7.2 / pH: 7.2
Buffer component
IDConc.NameFormulaBuffer ID
1150 mMsodium chlorideNaCl1
250 mMtris(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

-
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 FIELDBright-field microscopy / 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

-
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
12RELION2.03D reconstruction
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

+
About Yorodumi

-
News

-
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more