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- PDB-7k3v: Apoferritin structure at 1.34 angstrom resolution determined from... -

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Database: PDB / ID: 7k3v
TitleApoferritin structure at 1.34 angstrom resolution determined from a 300 kV Titan Krios G3i electron microscope with K3 detector
ComponentsFerritin heavy chain
KeywordsOXIDOREDUCTASE / Apoferritin / cryo-EM / atomic resolution / K3 detector
Function / homology
Function and homology information

intracellular ferritin complex / autolysosome / ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / negative regulation of fibroblast proliferation / ferric iron binding / ferrous iron binding / cellular iron ion homeostasis / iron ion transport ...intracellular ferritin complex / autolysosome / ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / negative regulation of fibroblast proliferation / ferric iron binding / ferrous iron binding / cellular iron ion homeostasis / iron ion transport / tertiary granule lumen / ficolin-1-rich granule lumen / immune response / iron ion binding / negative regulation of cell population proliferation / neutrophil degranulation / extracellular exosome / extracellular region / nucleus / cytosol / cytoplasm
Ferritin / Ferritin, conserved site / Ferritin-like / Ferritin-like superfamily / Ferritin-like diiron domain / Ferritin/DPS protein domain
Ferritin heavy chain
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 1.34 Å
AuthorsZhang, K. / Pintilie, G. / Li, S. / Schmid, M. / Chiu, W.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24GM129564 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM079429 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM103832 United States
CitationJournal: Cell Res / Year: 2020
Title: Resolving individual atoms of protein complex by cryo-electron microscopy.
Authors: Kaiming Zhang / Grigore D Pintilie / Shanshan Li / Michael F Schmid / Wah Chiu /
Validation Report
SummaryFull reportAbout validation report
DepositionSep 14, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2020Group: Data collection / Refinement description / Category: em_software / software
Item: _em_software.details / _em_software.name ..._em_software.details / _em_software.name / _em_software.version / _software.name / _software.version

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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
hetero molecules

Theoretical massNumber of molelcules
Total (without water)501,250358

TypeNameSymmetry operationNumber
identity operation1_5551


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

Mass: 20116.547 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FTH1, FTH, FTHL6, OK/SW-cl.84, PIG15
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P02794, ferroxidase
#2: Chemical...
ChemComp-ZN / ZINC ION / Zinc

Mass: 65.409 Da / Num. of mol.: 254 / Source method: obtained synthetically / Formula: Zn
#3: Chemical...
ChemComp-NA / SODIUM ION / Sodium

Mass: 22.990 Da / Num. of mol.: 80 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water

Mass: 18.015 Da / Num. of mol.: 2672 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

Experimental details


EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

Sample preparation

ComponentName: ApoferritinFerritin / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.48 MDa / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Buffer solutionpH: 8 / Details: 50 mM Tris-HCl (pH 8.0), 150 mM NaCl
SpecimenConc.: 1.5 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 R2/1
VitrificationCryogen name: ETHANE

Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1000 nm / Nominal defocus min: 300 nm / Calibrated defocus min: 100 nm / Calibrated defocus max: 1500 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Image recordingAverage exposure time: 0.5 sec. / Electron dose: 45 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 8034
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 15 eV


SoftwareName: Segger / Version: 2.5.2 / Classification: refinement
EM software
1EMAN2.3particle selection
2EPU2.7image acquisition
4CTFFIND4CTF correction
7UCSF Chimera1.13model fittinghttps://www.cgl.ucsf.edu/chimera/
12RELION3.13D reconstruction
13PHENIX1.18.2_3874model refinementphenix.real_space_refine
Particle selectionNum. of particles selected: 1176336
SymmetryPoint symmetry: O (octahedral)
3D reconstructionResolution: 1.34 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 902455 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL / Target criteria: CC
Atomic model buildingPDB-ID: 3AJO
Pdb chain-ID: A

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