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- EMDB-30205: Cryo-EM reconstruction of equine apoferritin (4 mM PEG8) -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-30205
TitleCryo-EM reconstruction of equine apoferritin (4 mM PEG8)
Map data
Sample
  • Complex: equine apoferritin (4 mM PEG8)
Function / homology
Function and homology information


ferritin complex / autolysosome / : / ferric iron binding / autophagosome / ferrous iron binding / iron ion transport / cytoplasmic vesicle / 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: 3.0 Å
AuthorsZhang Z / Ohto U / Shimizu T
CitationJournal: Structure / Year: 2021
Title: Improving particle quality in cryo-EM analysis using a PEGylation method.
Authors: Zhikuan Zhang / Hideki Shigematsu / Toshiyuki Shimizu / Umeharu Ohto /
Abstract: Cryo-electron microscopy (cryo-EM) is widely used for structural biology studies and has been developed extensively in recent years. However, its sample vitrification process is a major limitation ...Cryo-electron microscopy (cryo-EM) is widely used for structural biology studies and has been developed extensively in recent years. However, its sample vitrification process is a major limitation because it causes severe particle aggregation and/or denaturation. This effect is thought to occur because particles tend to stick to the "deadly" air-water interface during vitrification. Here, we report a method for PEGylation of proteins that can efficiently protect particles against such problems during vitrification. This method alleviates the laborious process of fine-tuning the vitrification conditions, allowing for analysis of samples that would otherwise be discarded.
History
DepositionApr 8, 2020-
Header (metadata) releaseJun 16, 2021-
Map releaseJun 16, 2021-
UpdateOct 27, 2021-
Current statusOct 27, 2021Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.066
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.066
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30205.png

Downloads & links

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Map

FileDownload / File: emd_30205.map.gz / Format: CCP4 / Size: 28.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.23 Å/pix.
x 196 pix.
= 240.8 Å		1.23 Å/pix.
x 196 pix.
= 240.8 Å		1.23 Å/pix.
x 196 pix.
= 240.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.22857 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.066 / Movie #1: 0.066
Minimum - Maximum-0.14140262 - 0.30406287
Average (Standard dev.)4.4901913e-05 (±0.016760426)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions196196196
Spacing196196196
CellA=B=C: 240.79971 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.22857142857141.22857142857141.2285714285714
M x/y/z196196196
origin x/y/z0.0000.0000.000
length x/y/z240.800240.800240.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS196196196
D min/max/mean-0.1410.3040.000

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Supplemental data

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Sample components

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Entire : equine apoferritin (4 mM PEG8)

EntireName: equine apoferritin (4 mM PEG8)
Components
  • Complex: equine apoferritin (4 mM PEG8)

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Supramolecule #1: equine apoferritin (4 mM PEG8)

SupramoleculeName: equine apoferritin (4 mM PEG8) / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Equus caballus (horse)

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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: 7.7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 11723
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT

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