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- EMDB-9599: Cryo-EM structure of mouse heavy-chain apoferritin at 1.62 A -

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Basic information

Entry
Database: EMDB / ID: EMD-9599
TitleCryo-EM structure of mouse heavy-chain apoferritin at 1.62 A
Map datamouse heavy chain apoferritin sharpened map
Sample
  • Complex: apoferritin
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.62 Å
AuthorsDanev R / Yanagisawa H / Kikkawa M
Funding support Japan, 1 items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED) Japan
CitationJournal: Trends Biochem Sci / Year: 2019
Title: Cryo-Electron Microscopy Methodology: Current Aspects and Future Directions.
Authors: Radostin Danev / Haruaki Yanagisawa / Masahide Kikkawa /
Abstract: Cryo-electron microscopy (cryo-EM) has emerged as a powerful structure determination technique. Its most prolific branch is single particle analysis (SPA), a method being used in a growing number of ...Cryo-electron microscopy (cryo-EM) has emerged as a powerful structure determination technique. Its most prolific branch is single particle analysis (SPA), a method being used in a growing number of laboratories worldwide to determine high-resolution protein structures. Cryo-electron tomography (cryo-ET) is another powerful approach that enables visualization of protein complexes in their native cellular environment. Despite the wide-ranging success of cryo-EM, there are many methodological aspects that could be improved. Those include sample preparation, sample screening, data acquisition, image processing, and structure validation. Future developments will increase the reliability and throughput of the technique and reduce the cost and skill level barrier for its adoption.
History
DepositionJul 27, 2018-
Header (metadata) releaseAug 8, 2018-
Map releaseAug 8, 2018-
UpdateAug 28, 2019-
Current statusAug 28, 2019Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.06
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.06
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9599.png

Downloads & links

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Map

FileDownload / File: emd_9599.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmouse heavy chain apoferritin sharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.52 Å/pix.
x 360 pix.
= 186.12 Å		0.52 Å/pix.
x 360 pix.
= 186.12 Å		0.52 Å/pix.
x 360 pix.
= 186.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.517 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06 / Movie #1: 0.06
Minimum - Maximum-0.1772024 - 0.31901142
Average (Standard dev.)-0.000007596358 (±0.016932437)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 186.12001 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.5170.5170.517
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z186.120186.120186.120
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ132132232
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.1770.319-0.000

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Supplemental data

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Mask #1

Fileemd_9599_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: mouse heavy chain apoferritin unfiltered half map 2

Fileemd_9599_half_map_1.map
Annotationmouse heavy chain apoferritin unfiltered half map 2
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: mouse heavy chain apoferritin unfiltered half map 1

Fileemd_9599_half_map_2.map
Annotationmouse heavy chain apoferritin unfiltered half map 1
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

EntireName: apoferritin
Components
  • Complex: apoferritin

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Supramolecule #1: apoferritin

SupramoleculeName: apoferritin / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria) / Recombinant strain: BL21(DE3)
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

Concentration4 mg/mL
BufferpH: 7
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Details: JEOL Ion Bombarder on Soft setting
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 4 K / Instrument: FEI VITROBOT MARK IV / Details: blot for 5 s.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Alignment procedureComa free - Residual tilt: 0.02 mrad
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Sampling interval: 15.0 µm / Number grids imaged: 1 / Number real images: 1647 / Average exposure time: 18.21 sec. / Average electron dose: 50.0 e/Å2 / Details: Exposure rate 0.74 e/pix/s
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus max: 1.3 µm / Calibrated defocus min: 0.2 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.3 µm / Nominal defocus min: 0.2 µm / Nominal magnification: 155000
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: 200000
CTF correctionSoftware:
Namedetails
Gctf (ver. 1.18b1)initial CTF fits
RELION (ver. 3.0b)CTF refinement
Startup modelType of model: OTHER / Details: from a previous dataset
Final reconstructionApplied symmetry - Point group: O (octahedral) / Resolution.type: BY AUTHOR / Resolution: 1.62 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0b) / Number images used: 147000
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0b)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0b)

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Atomic model buiding 1

Initial modelPDB ID:

2cih

RefinementProtocol: RIGID BODY FIT

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