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- EMDB-3854: Cryo-EM structure of human apoferritin at 3.15 A resolution deter... -

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Basic information

Entry
Database: EMDB / ID: 3854
TitleCryo-EM structure of human apoferritin at 3.15 A resolution determined with the Volta phase plate
Samplehuman h-ferritin
SourceHomo sapiens / human
Map dataCryo-EM structure of human apoferritin at 3.15 A determined with the Volta phase plate
Methodsingle particle reconstruction, at 3.15 Å resolution
AuthorsPechnikova EV
CitationTo Be Published

To Be Published Search PubMed
Cryo-EM structure of human apoferritin at 3.15 A resolution determined with the Volta phase plate
Pechnikova EV

DateDeposition: Aug 25, 2017 / Header (metadata) release: Nov 8, 2017 / Map release: Nov 8, 2017 / Last update: Nov 8, 2017

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Structure visualization

Movie
  • Surface view colored by radius
  • Surface level: 0.1
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with section colored by density value
  • Surface level: 0.1
  • Imaged by UCSF CHIMERA
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Supplemental images

Downloads & links

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Map

Fileemd_3854.map.gz (map file in CCP4 format, 32001 KB)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
200 pix
0.82 Å/pix.
= 164. Å
200 pix
0.82 Å/pix.
= 164. Å
200 pix
0.82 Å/pix.
= 164. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 0.82 Å
Density
Contour Level:0.1 (by author), 0.1 (movie #1):
Minimum - Maximum-0.50788814 - 0.61861026
Average (Standard dev.)0.0023143764 (0.05956288)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions200200200
Origin000
Limit199199199
Spacing200200200
CellA=B=C: 164 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.820.820.82
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z164.000164.000164.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.5080.6190.002

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Supplemental data

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Sample components

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Entire human h-ferritin

EntireName: human h-ferritin
Details: The sample was prepared in National Laboratory of Biomacromolecules, IBP, China
Number of components: 2
MassTheoretical: 509 kDa

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Component #1: protein, human h-ferritin

ProteinName: human h-ferritin
Details: The sample was prepared in National Laboratory of Biomacromolecules, IBP, China
Recombinant expression: No
MassTheoretical: 509 kDa
SourceSpecies: Homo sapiens / human
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #2: protein, human h-ferritin

ProteinName: human h-ferritin / Recombinant expression: No
Source (engineered)Expression System: Homo sapiens / human

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionBuffer solution: PBS / pH: 7.4
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %

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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: 58 e/Å2 / Illumination mode: OTHER
LensMagnification: 96000 X (nominal) / Cs: 2.7 mm / Imaging mode: OTHER
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: OTHER

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: O (octahedral) / Number of projections: 8396
3D reconstructionSoftware: RELION / Resolution: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution assessment)

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Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

  • Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
  • Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
  • Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.

External links: The 2017 Nobel Prize in Chemistry - Press Release

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