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- EMDB-44779: Human light chain ferritin reacted with iron (3 Fe2+ to ferritin ... -

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Basic information

Entry
Database: EMDB / ID: EMD-44779
TitleHuman light chain ferritin reacted with iron (3 Fe2+ to ferritin monomer ratio). Reconstruction of particles with one nanoparticle.
Map dataHuman light chain ferritin reacted with Ferrous salt(3 Fe2 per ferritin subunit) .Map based on 2D classes which show one iron nanoparticle per ferritin cage.
Sample
  • Complex: Human Light Chain Ferritin
    • Protein or peptide: Ferritin light chain
KeywordsIron oxide binding protein / METAL BINDING PROTEIN
Function / homology
Function and homology information


ferritin complex / Scavenging by Class A Receptors / Golgi Associated Vesicle Biogenesis / autolysosome / ferric iron binding / autophagosome / iron ion transport / Iron uptake and transport / ferrous iron binding / azurophil granule lumen ...ferritin complex / Scavenging by Class A Receptors / Golgi Associated Vesicle Biogenesis / autolysosome / ferric iron binding / autophagosome / iron ion transport / Iron uptake and transport / ferrous iron binding / azurophil granule lumen / intracellular iron ion homeostasis / iron ion binding / Neutrophil degranulation / extracellular exosome / 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 light chain
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.85 Å
AuthorsSen S / Nannenga BL / Williams D
Funding support United States, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1942084 United States
CitationJournal: J Am Chem Soc / Year: 2025
Title: Observation of the Protein-Inorganic Interface of Ferritin by Cryo-Electron Microscopy.
Authors: Sagnik Sen / Amar Thaker / Alison Haymaker / Dewight Williams / Po-Lin Chiu / Brent L Nannenga /
Abstract: Visualizing the structure of the protein-inorganic interface is critically important for a more complete understanding of biomineralization. Unfortunately, there are limited approaches for the direct ...Visualizing the structure of the protein-inorganic interface is critically important for a more complete understanding of biomineralization. Unfortunately, there are limited approaches for the direct and detailed study of biomolecules that interact with inorganic materials. Here, we use single-particle cryo-electron microscopy (cryo-EM) to study the protein-nanoparticle (NP) interactions of human light chain ferritin and visualize the high-resolution details of the protein-inorganic interface. In this work, we determined the 2.85 Å structure of human light chain ferritin bound to its native iron oxide NP substrate. The resulting cryo-EM maps confirmed and enhanced previously proposed interactions of the protein with the material along the B-helix and revealed new interaction at the C-terminus of light chain ferritin. This work sheds new light on the mechanisms of ferritin biomineralization and further demonstrates the application of cryo-EM for the study of protein-inorganic systems.
History
DepositionMay 7, 2024-
Header (metadata) releaseMay 14, 2025-
Map releaseMay 14, 2025-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44779.png

Downloads & links

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Map

FileDownload / File: emd_44779.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHuman light chain ferritin reacted with Ferrous salt(3 Fe2 per ferritin subunit) .Map based on 2D classes which show one iron nanoparticle per ferritin cage.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 256 pix.
= 263.68 Å		1.03 Å/pix.
x 256 pix.
= 263.68 Å		1.03 Å/pix.
x 256 pix.
= 263.68 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.03 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.191
Minimum - Maximum-0.17241776 - 0.61838377
Average (Standard dev.)0.0040384308 (±0.03396862)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 263.68 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_44779_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_44779_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : Human Light Chain Ferritin

EntireName: Human Light Chain Ferritin
Components
  • Complex: Human Light Chain Ferritin
    • Protein or peptide: Ferritin light chain

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Supramolecule #1: Human Light Chain Ferritin

SupramoleculeName: Human Light Chain Ferritin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 480 KDa

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Macromolecule #1: Ferritin light chain

MacromoleculeName: Ferritin light chain / type: protein_or_peptide / ID: 1 / Number of copies: 24 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 19.917486 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SSQIRQNYST DVEAAVNSLV NLYLQASYTY LSLGFYFDRD DVALEGVSHF FRELAEEKRE GYERLLKMQN QRGGRALFQD IKKPAEDEW GKTPDAMKAA MALEKKLNQA LLDLHALGSA RTDPHLCDFL ETHFLDEEVK LIKKMGDHLT NLHRLGGPEA G LGEYLFER LTLKHD

UniProtKB: Ferritin light chain

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 9.06 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 0.1 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.85 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 123544
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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