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- EMDB-44401: H-rich (70%H:30%L) human heteropolymeric ferritin -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-44401
TitleH-rich (70%H:30%L) human heteropolymeric ferritin
Map dataH-rich (70%H:30%L) human heteropolymer ferritin
Sample
  • Complex: human heteropolymer apoferritin
Keywordsheteropolymer ferritin / METAL BINDING PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.5 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_44401.png

Downloads & links

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Map

FileDownload / File: emd_44401.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationH-rich (70%H:30%L) human heteropolymer ferritin
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.95 Å/pix.
x 300 pix.
= 285. Å		0.95 Å/pix.
x 300 pix.
= 285. Å		0.95 Å/pix.
x 300 pix.
= 285. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.95 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.0
Minimum - Maximum-3.479375 - 7.293637
Average (Standard dev.)0.014545586 (±0.31972912)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 285.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_44401_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_44401_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 apoferritin

EntireName: human heteropolymer apoferritin
Components
  • Complex: human heteropolymer apoferritin

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Supramolecule #1: human heteropolymer apoferritin

SupramoleculeName: human heteropolymer apoferritin / type: complex / ID: 1 / Parent: 0 / Details: H-rich (70%H:30%L) human heteropolymer 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
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm

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Image processing

Startup modelType of model: INSILICO MODEL / In silico model: Ab initio model
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 114720
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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