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- EMDB-44400: L-rich (38%H:62%L) human heteropolymeric ferritin -

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Basic information

Entry
Database: EMDB / ID: EMD-44400
TitleL-rich (38%H:62%L) human heteropolymeric ferritin
Map dataL-rich (38%H:62%L human heteropolymeric ferritin)
Sample
  • Complex: human heteropolymer ferritin
Keywordsheteropolymer ferritin / METAL BINDING PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsBou-Abdallah F / Terashi G
Funding support United States, 7 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1934666 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM133840 United States
National Science Foundation (NSF, United States)DBI2003635 United States
National Science Foundation (NSF, United States)DBI2146026 United States
National Science Foundation (NSF, United States)IIS2211598 United States
National Science Foundation (NSF, United States)DMS2151678 United States
National Science Foundation (NSF, United States)CMMI1825941 United States
CitationJournal: Protein Sci / Year: 2024
Title: Unveiling the stochastic nature of human heteropolymer ferritin self-assembly mechanism.
Authors: Fadi Bou-Abdallah / Jeremie Fish / Genki Terashi / Yuanyuan Zhang / Daisuke Kihara / Paolo Arosio /
Abstract: Despite ferritin's critical role in regulating cellular and systemic iron levels, our understanding of the structure and assembly mechanism of isoferritins, discovered over eight decades ago, remains ...Despite ferritin's critical role in regulating cellular and systemic iron levels, our understanding of the structure and assembly mechanism of isoferritins, discovered over eight decades ago, remains limited. Unveiling how the composition and molecular architecture of hetero-oligomeric ferritins confer distinct functionality to isoferritins is essential to understanding how the structural intricacies of H and L subunits influence their interactions with cellular machinery. In this study, ferritin heteropolymers with specific H to L subunit ratios were synthesized using a uniquely engineered plasmid design, followed by high-resolution cryo-electron microscopy analysis and deep learning-based amino acid modeling. Our structural examination revealed unique architectural features during the self-assembly mechanism of heteropolymer ferritins and demonstrated a significant preference for H-L heterodimer formation over H-H or L-L homodimers. Unexpectedly, while dimers seem essential building blocks in the protein self-assembly process, the overall mechanism of ferritin self-assembly is observed to proceed randomly through diverse pathways. The physiological significance of these findings is discussed including how ferritin microheterogeneity could represent a tissue-specific adaptation process that imparts distinctive tissue-specific functions to isoferritins.
History
DepositionApr 3, 2024-
Header (metadata) releaseJul 24, 2024-
Map releaseJul 24, 2024-
UpdateJul 24, 2024-
Current statusJul 24, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44400.png

Downloads & links

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Map

FileDownload / File: emd_44400.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationL-rich (38%H:62%L human heteropolymeric ferritin)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 256 pix.
= 281.6 Å		1.1 Å/pix.
x 256 pix.
= 281.6 Å		1.1 Å/pix.
x 256 pix.
= 281.6 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.013782844 - 0.04981896
Average (Standard dev.)0.000056797293 (±0.0033060478)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 281.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_44400_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_44400_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : human heteropolymer ferritin

EntireName: human heteropolymer ferritin
Components
  • Complex: human heteropolymer ferritin

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Supramolecule #1: human heteropolymer ferritin

SupramoleculeName: human heteropolymer ferritin / type: complex / ID: 1 / Parent: 0 / Details: L-rich (38%H:62%L) human heteropolymeric ferritin
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 500 KDa

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 42.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 74014
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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