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- EMDB-44797: C-terminus truncated (last two residues) mutant of Human light ch... -

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Basic information

Entry
Database: EMDB / ID: EMD-44797
TitleC-terminus truncated (last two residues) mutant of Human light chain ferritin reacted with iron (3 Fe2+ to ferritin monomer ratio). Reconstruction of particles with no nanoparticle.
Map dataC-terminus truncated (last two residues) mutant of Human light chain ferritin reacted with Ferrous salt(3 Fe2 per ferritin subunit) .Map based on 2D classes which show no iron nanoparticle.
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 uptake and transport / ferrous iron binding / azurophil granule lumen / iron ion transport ...ferritin complex / Scavenging by Class A Receptors / Golgi Associated Vesicle Biogenesis / autolysosome / ferric iron binding / autophagosome / Iron uptake and transport / ferrous iron binding / azurophil granule lumen / iron ion transport / intracellular iron ion homeostasis / iron ion binding / Neutrophil degranulation / extracellular exosome / extracellular region / identical protein binding / membrane / 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 light chain
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.36 Å
AuthorsSen S / Nannenga BL / Williams D
Funding support United States, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) 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 9, 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_44797.png

Downloads & links

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Map

FileDownload / File: emd_44797.map.gz / Format: CCP4 / Size: 25.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationC-terminus truncated (last two residues) mutant of Human light chain ferritin reacted with Ferrous salt(3 Fe2 per ferritin subunit) .Map based on 2D classes which show no iron nanoparticle.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 188 pix.
= 193.64 Å		1.03 Å/pix.
x 188 pix.
= 193.64 Å		1.03 Å/pix.
x 188 pix.
= 193.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.03 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.091
Minimum - Maximum-0.18245047 - 0.4292306
Average (Standard dev.)0.0037816549 (±0.033795495)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions188188188
Spacing188188188
CellA=B=C: 193.64 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map B.

Fileemd_44797_half_map_1.map
AnnotationHalf map B.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A.

Fileemd_44797_half_map_2.map
AnnotationHalf map A.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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: 474 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: 19.66425 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 LTLK

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

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 9.58 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: 2.36 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 381609
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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