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- EMDB-9890: Cryo-EM structure of human apoferritin at 1.9A resolution by CRYO... -

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Basic information

Entry
Database: EMDB / ID: EMD-9890
TitleCryo-EM structure of human apoferritin at 1.9A resolution by CRYO ARM 300
Map dataHuman apoferritin from E. coli
Sample
  • Cell: apoferritin
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.9 Å
AuthorsHamaguchi T / Maki-Yonekura S / Naitow H / Matsuura Y / Ishikawa T / Yonekura K
Funding support Japan, 4 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science16H04757 Japan
Japan Agency for Medical Research and Development (AMED)the Cyclic Innovation for Clinical Empowerment (CiCLE) Japan
Japan Society for the Promotion of Science24657111 Japan
Japan Science and TechnologySENTAN Japan
CitationJournal: J Struct Biol / Year: 2019
Title: A new cryo-EM system for single particle analysis.
Authors: Tasuku Hamaguchi / Saori Maki-Yonekura / Hisashi Naitow / Yoshinori Matsuura / Tetsuya Ishikawa / Koji Yonekura /
Abstract: A new cryo-EM system has been investigated for single particle analysis of protein structures. The system provides parallel illumination of a highly-coherent 300 kV electron beam from a cold-field ...A new cryo-EM system has been investigated for single particle analysis of protein structures. The system provides parallel illumination of a highly-coherent 300 kV electron beam from a cold-field emission gun, and boosts image contrast with an in-column energy filter and a hole-free phase plate. It includes motorized cryo-sample loading and automated liquid-nitrogen filling for cooling multiple samples. In this study, we describe gun and electron beam characteristics, and demonstrate the suitability of this system for single particle reconstructions. The performance of the system is tested on two examples, a spherical virus and apoferritin. GUI programs have also been developed to control and monitor the system for correct illumination, imaging with less ellipticity and steady magnification, and timing of flashing and liquid-nitrogen filling. These programs are especially useful for efficient application of the system to single particle cryo-EM.
History
DepositionApr 19, 2019-
Header (metadata) releaseMay 15, 2019-
Map releaseMay 15, 2019-
UpdateJun 19, 2019-
Current statusJun 19, 2019Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.023
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.023
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9890.png

Downloads & links

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Map

FileDownload / File: emd_9890.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHuman apoferritin from E. coli
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.5 Å/pix.
x 512 pix.
= 253.44 Å		0.5 Å/pix.
x 512 pix.
= 253.44 Å		0.5 Å/pix.
x 512 pix.
= 253.44 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.495 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.023 / Movie #1: 0.023
Minimum - Maximum-0.036023274 - 0.07791148
Average (Standard dev.)-0.00000079373393 (±0.00424428)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 253.44 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.4950.4950.495
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z253.440253.440253.440
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ858858858
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS512512512
D min/max/mean-0.0360.078-0.000

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Supplemental data

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Sample components

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Entire : apoferritin

EntireName: apoferritin
Components
  • Cell: apoferritin

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Supramolecule #1: apoferritin

SupramoleculeName: apoferritin / type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)

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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

Concentration3.5 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Specialist opticsEnergy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-50 / Number real images: 1292 / Average exposure time: 10.0 sec. / Average electron dose: 101.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 150.0 µm / Calibrated defocus max: 12.0 µm / Calibrated defocus min: 2.5 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 13.0 µm / Nominal defocus min: 3.0 µm / Nominal magnification: 100000
Sample stageSpecimen holder model: JEOL / Cooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 210065
CTF correctionSoftware - Name: CTFFIND (ver. 4.1.10)
Final reconstructionApplied symmetry - Point group: O (octahedral) / Resolution.type: BY AUTHOR / Resolution: 1.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 36855
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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