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- EMDB-9914: Cryo-EM structure of mouse heavy-chain apoferritin at 2.01 A -

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Basic information

Entry
Database: EMDB / ID: EMD-9914
TitleCryo-EM structure of mouse heavy-chain apoferritin at 2.01 A
Map data
Sample
  • Complex: apo-ferritin
    • Protein or peptide: Mus musculus ferritin heavy polypeptide 1
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.01 Å
AuthorsYanagisawa H / Danev R / Kikkawa M
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
DepositionMay 23, 2019-
Header (metadata) releaseJun 12, 2019-
Map releaseJun 12, 2019-
UpdateJun 24, 2020-
Current statusJun 24, 2020Processing 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
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9914.png

Downloads & links

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Map

FileDownload / File: emd_9914.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.79 Å/pix.
x 320 pix.
= 251.456 Å		0.79 Å/pix.
x 320 pix.
= 251.456 Å		0.79 Å/pix.
x 320 pix.
= 251.456 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.7858 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06 / Movie #1: 0.06
Minimum - Maximum-0.101347044 - 0.22254306
Average (Standard dev.)0.0000064896 (±0.010315774)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 251.456 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.78580.78580.7858
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z251.456251.456251.456
α/β/γ90.00090.00090.000
start NX/NY/NZ-200-200-200
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.1010.2230.000

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Supplemental data

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Sample components

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Entire : apo-ferritin

EntireName: apo-ferritin
Components
  • Complex: apo-ferritin
    • Protein or peptide: Mus musculus ferritin heavy polypeptide 1

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Supramolecule #1: apo-ferritin

SupramoleculeName: apo-ferritin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: mouse ferritin heavy chain, 24 mer
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant strain: BL21(DE3) pLys
Molecular weightTheoretical: 440 KDa

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Macromolecule #1: Mus musculus ferritin heavy polypeptide 1

MacromoleculeName: Mus musculus ferritin heavy polypeptide 1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO / EC number: ferroxidase
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MTTASPSQVR QNYHQDAEAA INRQINLELY ASYVYLSMSC YFDRDDVALK NFAKYFLHQS HEEREHAEKL MKLQNQRGGR IFLQDIKKPD RDDWESGLNA MECALHLEKS VNQSLLELHK LATDKNDPHL CDFIETYYLS EQVKSIKELG DHVTNLRKMG APEAGMAEYL FDKHTLGHGD ES

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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

Concentration7 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
30.0 mMC8H18N2O4SHepes
0.3 MNaClsodium chloride
1.0 mMC4H10O2S2dithiothreitol
GridModel: Quantifoil R1.2/1.3 / Material: COPPER/RHODIUM / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 279 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 30 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 1-40 / Number grids imaged: 1 / Number real images: 1109 / Average exposure time: 3.0 sec. / Average electron dose: 1.348 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus max: 1.8 µm / Calibrated defocus min: 0.4 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 165000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: Gctf (ver. 1.18b2)
Final reconstructionApplied symmetry - Point group: O (octahedral) / Resolution.type: BY AUTHOR / Resolution: 2.01 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 323292
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
FSC plot (resolution estimation)

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