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- EMDB-44398: L-rich (38%H:62%L) human heteropolymeric ferritin -

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Basic information

Entry
Database: EMDB / ID: EMD-44398
TitleL-rich (38%H:62%L) human heteropolymeric ferritin
Map data
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: To Be Published
Title: Unveiling the Stochastic Nature of Human Heteropolymer Ferritin Self-Assembly Mechanism
Authors: Bou-Abdallah F / Terashi G
History
DepositionApr 3, 2024-
Header (metadata) releaseDec 4, 2024-
Map releaseDec 4, 2024-
UpdateDec 4, 2024-
Current statusDec 4, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44398.png

Downloads & links

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Map

FileDownload / File: emd_44398.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
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

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.013937188 - 0.05322458
Average (Standard dev.)0.0001581141 (±0.0034171075)
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_44398_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_44398_half_map_2.map
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 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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