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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 / ferroxidase / autolysosome / negative regulation of ferroptosis / ferroxidase activity / negative regulation of fibroblast proliferation / endocytic vesicle lumen / Neutrophil degranulation / ferric iron binding ...Iron uptake and transport / Golgi Associated Vesicle Biogenesis / ferroxidase / autolysosome / negative regulation of ferroptosis / 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 / cytosol / cytoplasm
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: IUCrJ / Year: 2026
Title: Atomic resolution cryo-EM at 200 keV.
Authors: Radostin Danev / Haruaki Yanagisawa / Keitaro Yamashita / Fabian Eisenstein / Masahide Kikkawa /
Abstract: Atomic resolution in cryo-electron microscopy was first demonstrated six years ago. This was accomplished using 300 kV electron microscopes equipped with new hardware that provided narrower energy ...Atomic resolution in cryo-electron microscopy was first demonstrated six years ago. This was accomplished using 300 kV electron microscopes equipped with new hardware that provided narrower energy spread, aberration correction and energy filtering. Here, we report the achievement of 1.24 Å atomic resolution on an upgraded 200 kV electron microscope featuring a cold field emission gun, a high-resolution objective lens polepiece and an energy filter. These components transform the instrument into a cost-effective single-particle cryo-EM platform with performance comparable to that of significantly more expensive 300 kV systems. The microscope can also be operated at 100 kV and by using a high-speed hybrid-pixel detector we were able to reach sub-2 Å resolution.
History
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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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