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- PDB-23wj: Subtomogram average of Apoferrtin (11x11) using CRYO ARM 300II -

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Basic information

Entry
Database: PDB / ID: 23wj
TitleSubtomogram average of Apoferrtin (11x11) using CRYO ARM 300II
ComponentsFerritin heavy chain, N-terminally processed
KeywordsRECOMBINATION / Apoferrtin
Function / homology
Function and homology information


Iron uptake and transport / Golgi Associated Vesicle Biogenesis / ferroxidase / negative regulation of ferroptosis / autolysosome / ferroxidase activity / negative regulation of fibroblast proliferation / endocytic vesicle lumen / Neutrophil degranulation / ferric iron binding ...Iron uptake and transport / Golgi Associated Vesicle Biogenesis / ferroxidase / negative regulation of ferroptosis / autolysosome / ferroxidase activity / negative regulation of fibroblast proliferation / endocytic vesicle lumen / Neutrophil degranulation / ferric iron binding / autophagosome / iron ion transport / ferrous iron binding / intracellular iron ion homeostasis / immune response / iron ion binding / negative regulation of cell population proliferation / mitochondrion / extracellular region / membrane / identical protein binding / 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
: / Ferritin heavy chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 2.1 Å
AuthorsYanagisawa, H. / Eisenstein, F. / Miyata, T. / Kinoshita, M. / Kikkawa, M. / Namba, K. / Makino, F.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP22am121003 Japan
Japan Agency for Medical Research and Development (AMED)JP17pc0101020 Japan
CitationJournal: AIMS Biophysics / Year: 2026
Title: Subtomogram averaging by cryo electron tomography using CRYO ARMTM 300 II for purified and cellular samples
Authors: Makino, F. / Yanagisawa, H. / Eisenstein, F. / Miyata, T. / Kinoshita, M. / Kikkawa, M. / Namba, K.
History
DepositionFeb 23, 2026Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 22, 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, N-terminally processed
B: Ferritin heavy chain, N-terminally processed
C: Ferritin heavy chain, N-terminally processed
D: Ferritin heavy chain, N-terminally processed
E: Ferritin heavy chain, N-terminally processed
F: Ferritin heavy chain, N-terminally processed
G: Ferritin heavy chain, N-terminally processed
H: Ferritin heavy chain, N-terminally processed
I: Ferritin heavy chain, N-terminally processed
J: Ferritin heavy chain, N-terminally processed
K: Ferritin heavy chain, N-terminally processed
L: Ferritin heavy chain, N-terminally processed
M: Ferritin heavy chain, N-terminally processed
N: Ferritin heavy chain, N-terminally processed
O: Ferritin heavy chain, N-terminally processed
P: Ferritin heavy chain, N-terminally processed
Q: Ferritin heavy chain, N-terminally processed
R: Ferritin heavy chain, N-terminally processed
S: Ferritin heavy chain, N-terminally processed
T: Ferritin heavy chain, N-terminally processed
U: Ferritin heavy chain, N-terminally processed
V: Ferritin heavy chain, N-terminally processed
W: Ferritin heavy chain, N-terminally processed
X: Ferritin heavy chain, N-terminally processed
hetero molecules


Theoretical massNumber of molelcules
Total (without water)483,81554
Polymers481,91024
Non-polymers1,90530
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein ...
Ferritin heavy chain, N-terminally processed


Mass: 20079.594 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Fth1, Fth / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P09528
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe
#3: Chemical...
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: subtomogram averaging

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Sample preparation

ComponentName: Mouse apoferritin / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.5
SpecimenConc.: 4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 50000 X / Calibrated magnification: 49505 X / Nominal defocus max: 3000 nm / Nominal defocus min: 2000 nm / Cs: 2.7 mm
Specimen holderSpecimen holder model: JEOL CRYOSPECPORTER
Image recordingElectron dose: 3.5 e/Å2 / Avg electron dose per subtomogram: 137 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)
EM imaging opticsEnergyfilter name: In-column Omega Filter / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
1RELION5volume selection
2PHENIXmodel refinement
5RELION5CTF correction
11RELION5final Euler assignment
12RELION5classification
13RELION53D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: O (octahedral)
3D reconstructionResolution: 2.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 154717 / Symmetry type: POINT
EM volume selectionNum. of tomograms: 117 / Num. of volumes extracted: 158180
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 6.83 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002534512
ELECTRON MICROSCOPYf_angle_d0.475846416
ELECTRON MICROSCOPYf_chiral_restr0.03614848
ELECTRON MICROSCOPYf_plane_restr0.00366096
ELECTRON MICROSCOPYf_dihedral_angle_d4.54054512

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