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

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Basic information

Database: EMDB / ID: 9599
TitleCryo-EM structure of mouse heavy-chain apoferritin at 1.62 A
Map datamouse heavy chain apoferritin sharpened map
SourceMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / 1.62 Å resolution
AuthorsDanev R / Yanagisawa H / Kikkawa M
CitationJournal: To Be Published
Title: Cryo-EM structure of mouse heavy-chain apoferritin at 1.62 A
Authors: Danev R / Yanagisawa H / Kikkawa M
DateDeposition: Jul 27, 2018 / Header (metadata) release: Aug 8, 2018 / Map release: Aug 8, 2018 / Last update: Aug 8, 2018

Structure visualization

  • 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
  • Download
  • Surface view colored by radius
  • Surface level: 0.06
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
Supplemental images

Downloads & links


Fileemd_9599.map.gz (map file in CCP4 format, 186625 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
360 pix
0.52 Å/pix.
= 186.12 Å
360 pix
0.52 Å/pix.
= 186.12 Å
360 pix
0.52 Å/pix.
= 186.12 Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.517 Å
Contour Level:0.06 (by author), 0.06 (movie #1):
Minimum - Maximum-0.1772024 - 0.31901142
Average (Standard dev.)-0.000007596358 (0.016932437)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA=B=C: 186.12001 Å
α=β=γ: 90.0 deg.

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
start NX/NY/NZ000
MAP C/R/S123
start NC/NR/NS000
D min/max/mean-0.1770.319-0.000

Supplemental data

Mask #1

Projections & Slices
Slices (1/2)
Density Histograms

Sample components

Entire apoferritin

EntireName: apoferritin / Number of components: 1

Component #1: protein, apoferritin

ProteinName: apoferritinFerritin / Recombinant expression: No
MassTheoretical: 500 kDa
SourceSpecies: Mus musculus (house mouse)
Source (engineered)Expression System: Escherichia coli BL21(DE3) (bacteria) / Strain: BL21(DE3)

Experimental details

Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 4 mg/ml / pH: 7
Support filmJEOL Ion Bombarder on Soft setting
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 4 K / Humidity: 95 % / Details: blot for 5 s.

Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 5 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 155000. X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 200.0 - 1300.0 nm
CameraDetector: FEI FALCON III (4k x 4k)

Image acquisition

Image acquisitionNumber of digital images: 1647 / Sampling size: 15 microns / Details: Exposure rate 0.74 e/pix/s

Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: O (octahedral) / Number of projections: 147000
3D reconstructionResolution: 1.62 Å / Resolution method: FSC 0.143 CUT-OFF

Atomic model buiding

Modeling #1Refinement protocol: rigid body
Input PDB model: 2CIH

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