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- EMDB-3853: Cryo-EM structure of human apoferritin H -

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Basic information

Entry
Database: EMDB / ID: 3853
TitleCryo-EM structure of human apoferritin H
SampleHuman apoferritin H
SourceHomo sapiens / human
Map datahuman apoferritin H
Methodsingle particle reconstruction, at 2.5 Å resolution
AuthorsDudkina NV / Welsch S
CitationTo Be Published

To Be Published Search PubMed
Falcon 3 Electron Counting detector enables high resolution cryo-EM structures
Dudkina NV / Welsch S

DateDeposition: Aug 24, 2017 / Header (metadata) release: Sep 6, 2017 / Map release: Sep 6, 2017 / Last update: Sep 6, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.5
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 0.5
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

Downloads & links

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Map

Fileemd_3853.map.gz (map file in CCP4 format, 32001 KB)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
200 pix
1.06 Å/pix.
= 211.4 Å
200 pix
1.06 Å/pix.
= 211.4 Å
200 pix
1.06 Å/pix.
= 211.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.057 Å
Density
Contour Level:0.5 (by author), 0.5 (movie #1):
Minimum - Maximum-2.087887 - 2.6480424
Average (Standard dev.)-5.6675213E-5 (0.19209836)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions200200200
Origin000
Limit199199199
Spacing200200200
CellA=B=C: 211.40001 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0571.0571.057
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z211.400211.400211.400
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-2.0882.648-0.000

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Supplemental data

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Sample components

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Entire Human apoferritin H

EntireName: Human apoferritin H / Number of components: 2
MassTheoretical: 440 kDa

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Component #1: protein, Human apoferritin H

ProteinName: Human apoferritin H / Recombinant expression: No
MassTheoretical: 440 kDa
SourceSpecies: Homo sapiens / human
Source (engineered)Expression System: Escherichia coli bl21(de3) / bacteria / image: Escherichia coli

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Component #2: protein, Ferritin heavy chain

ProteinName: Ferritin heavy chain / 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 solutionpH: 7.4
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %
Details: Protein was applied to glow-discharged Quantifoil R2/2 grids

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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: 40 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 75000 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 500 - 3000 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: OTHER

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Image acquisition

Image acquisitionNumber of digital images: 203 / Sampling size: 14 microns

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: O (octahedral) / Number of projections: 37000
3D reconstructionSoftware: Relion / Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution assessment)

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