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- EMDB-25619: CryoEM map of horse spleen apoferritin determined using MeasureIc... -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-25619
TitleCryoEM map of horse spleen apoferritin determined using MeasureIce as a screening tool for ice thickness
Map data
Sample
  • Complex: Apoferritin from equine spleen
    • Protein or peptide: Ferritin light chain
Keywordsiron storage / complex / METAL BINDING PROTEIN
Function / homology
Function and homology information


ferritin complex / autolysosome / ferric iron binding / autophagosome / iron ion transport / ferrous iron binding / cytoplasmic vesicle / intracellular iron ion homeostasis / iron ion binding / 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 speciesEquus caballus (horse)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.88 Å
AuthorsHanssen E / Brown HG
Funding support Australia, 1 items
OrganizationGrant numberCountry
Not funded Australia
CitationJournal: Commun Biol / Year: 2022
Title: MeasureIce: accessible on-the-fly measurement of ice thickness in cryo-electron microscopy
Authors: Brown HG / Hanssen E
History
DepositionDec 5, 2021-
Header (metadata) releaseAug 24, 2022-
Map releaseAug 24, 2022-
UpdateJan 17, 2024-
Current statusJan 17, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_25619.png

Downloads & links

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Map

FileDownload / File: emd_25619.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.64 Å/pix.
x 440 pix.
= 280.28 Å		0.64 Å/pix.
x 440 pix.
= 280.28 Å		0.64 Å/pix.
x 440 pix.
= 280.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.637 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.1613838 - 0.3038219
Average (Standard dev.)0.000008000564 (±0.011759506)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 280.28 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_25619_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_25619_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_25619_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 : Apoferritin from equine spleen

EntireName: Apoferritin from equine spleen
Components
  • Complex: Apoferritin from equine spleen
    • Protein or peptide: Ferritin light chain

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Supramolecule #1: Apoferritin from equine spleen

SupramoleculeName: Apoferritin from equine spleen / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Equus caballus (horse)
Molecular weightTheoretical: 443 KDa

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Macromolecule #1: Ferritin light chain

MacromoleculeName: Ferritin light chain / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Equus caballus (horse)
SequenceString:
SQIRQNYSTE VEAAVNRLVN LYLRASYTYL SLGFYFDRDD VALEGVCHFF RELAEEKREG AERLLKMQNQ RGGRALFQDL QKPSQDEWGT TLDAMKAAIV LEKSLNQALL DLHALGSAQA DPHLCDFLES HFLDEEVKLI KKMGDHLTNI QRLVGSQAGL GEYLFERLTL K

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: 7.4 / Component - Name: PBS
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 619 / Average electron dose: 20.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 120000
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

Particle selectionNumber selected: 150669
Startup modelType of model: OTHER / Details: de novo
Final reconstructionApplied symmetry - Point group: O (octahedral) / Resolution.type: BY AUTHOR / Resolution: 1.88 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.2) / Number images used: 68025
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.2.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationNumber classes: 1
FSC plot (resolution estimation)

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