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- PDB-22fx: Cryo-EM structure of mouse heavy-chain apoferritin at 1.24 A on C... -

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Basic information

Entry
Database: PDB / ID: 22fx
TitleCryo-EM structure of mouse heavy-chain apoferritin at 1.24 A on CRYO ARM 200 II
ComponentsFerritin heavy chain
KeywordsMETAL BINDING PROTEIN / apoferritin
Function / homology
Function and homology information


Iron uptake and transport / Golgi Associated Vesicle Biogenesis / negative regulation of ferroptosis / ferroxidase / autolysosome / ferroxidase activity / negative regulation of fibroblast proliferation / Neutrophil degranulation / endocytic vesicle lumen / ferric iron binding ...Iron uptake and transport / Golgi Associated Vesicle Biogenesis / negative regulation of ferroptosis / ferroxidase / autolysosome / ferroxidase activity / negative regulation of fibroblast proliferation / Neutrophil degranulation / endocytic vesicle lumen / 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 / identical protein binding / membrane / 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 / single particle reconstruction / cryo EM / Resolution: 1.24 Å
AuthorsDanev, R. / Yanagisawa, H. / Yamashita, K. / Eisenstein, F. / Kikkawa, M.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)22H02554 Japan
Japan Agency for Medical Research and Development (AMED)JP25ama121002j0004 Japan
CitationJournal: To Be Published
Title: Atomic resolution cryo-EM at 200 keV
Authors: Danev, R. / Yanagisawa, H. / Yamashita, K. / Eisenstein, F. / Kikkawa, M.
History
DepositionJan 9, 2026Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 4, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Primary map / Data content type: Primary map / Provider: 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)21,2193
Polymers21,0981
Non-polymers1212
Water3,621201
1
A: Ferritin heavy chain
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)509,25372
Polymers506,34324
Non-polymers2,91048
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation23
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(-1), (1), (1)250.592
3generate(-1), (-1), (1)250.592, 250.592
4generate(1), (-1), (1)250.592
5generate(1), (1), (-1)250.592
6generate(-1), (1), (-1)250.592, 250.592
7generate(-1), (1), (1)250.592
8generate(-1), (1), (-1)250.592, 250.592
9generate(-1), (-1), (1)250.592, 250.592
10generate(1), (1), (1)
11generate(1), (1), (1)
12generate(-1), (-1), (-1)250.592, 250.592, 250.592
13generate(1), (1), (-1)250.592
14generate(-1), (-1), (1)250.592, 250.592
15generate(1), (-1), (-1)250.592, 250.592
16generate(-1), (1), (-1)250.592, 250.592
17generate(1), (-1), (-1)250.592, 250.592
18generate(-1), (-1), (-1)250.592, 250.592, 250.592
19generate(1), (-1), (1)250.592
20generate(1), (-1), (-1)250.592, 250.592
21generate(-1), (1), (1)250.592
22generate(1), (-1), (1)250.592
23generate(1), (1), (-1)250.592
24generate(-1), (-1), (-1)250.592, 250.592, 250.592

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Components

#1: Protein Ferritin heavy chain / Ferritin H subunit


Mass: 21097.631 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Fth1, Fth
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P09528, ferroxidase
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / Source method: isolated from a natural source / Formula: H2O
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: single particle reconstruction

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Sample preparation

ComponentName: homo 24-mer mouse heavy-chain apoferritin / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.5 MDa / Experimental value: NO
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Buffer solutionpH: 7.5
Details: 20 mM HEPES-NaOH pH 7.5, 300 mM NaCl, 1 mM dithiothreitol (DTT)
SpecimenConc.: 1.9 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: R0.6/1 / Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 278 K / Details: 3 ul sample, 20 s blot time

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 200
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 150000 X / Calibrated magnification: 163612 X / Nominal defocus max: 800 nm / Nominal defocus min: 200 nm / Calibrated defocus min: 200 nm / Calibrated defocus max: 800 nm / Cs: 1.5 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: JEOL CRYOSPECPORTER / Temperature (max): 87 K / Temperature (min): 87 K / Residual tilt: 0.5 mradians
Image recordingAverage exposure time: 1.51 sec. / Electron dose: 53.4 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 13654
EM imaging opticsEnergyfilter name: In-column Omega Filter / Energyfilter slit width: 20 eV
Image scansSampling size: 5 µm

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.5particle selection
2SerialEM4image acquisition
4cryoSPARC4.5CTF correction
7Cootmodel fitting
9Servalcatmodel refinement
10Cootmodel refinement
11cryoSPARC4.5initial Euler assignment
12cryoSPARC4.5final Euler assignment
13cryoSPARC4.5classification
14cryoSPARC4.53D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 652257
3D reconstructionResolution: 1.24 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 615248 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: RECIPROCAL
Atomic model buildingPDB-ID: 7A4M

7a4m


Accession code: 7A4M / Source name: PDB / Type: experimental model

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