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- EMDB-30100: 3.4A apoferritin from JEM-2100F + K2 Summit at 40K, RELION 3.0 pr... -

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Basic information

Entry
Database: EMDB / ID: EMD-30100
Title3.4A apoferritin from JEM-2100F + K2 Summit at 40K, RELION 3.0 processing, manual acquisition.
Map data3.4A apoferritin, JEM-2100F K2 Summit, 40K, RELION 3, manual acqusition, postprocessed map.
Sample
  • Complex: Apoferritin, 3.4A, JEM-2100F + K2 Summit, 40K, RELION 3.0
Function / homology
Function and homology information


ferric iron binding / iron ion transport / intracellular iron ion homeostasis
Similarity search - Function
Ferritin iron-binding regions signature 1. / Ferritin iron-binding regions signature 2. / Ferritin, conserved site / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsBurton-Smith RN / Kayama Y / Song C / Kato T / Murata K
CitationJournal: Sci Rep / Year: 2021
Title: Below 3 Å structure of apoferritin using a multipurpose TEM with a side entry cryoholder.
Authors: Yoko Kayama / Raymond N Burton-Smith / Chihong Song / Naoya Terahara / Takayuki Kato / Kazuyoshi Murata /
Abstract: Recently, the structural analysis of protein complexes by cryo-electron microscopy (cryo-EM) single particle analysis (SPA) has had great impact as a biophysical method. Many results of cryo-EM SPA ...Recently, the structural analysis of protein complexes by cryo-electron microscopy (cryo-EM) single particle analysis (SPA) has had great impact as a biophysical method. Many results of cryo-EM SPA are based on data acquired on state-of-the-art cryo-electron microscopes customized for SPA. These are currently only available in limited locations around the world, where securing machine time is highly competitive. One potential solution for this time-competitive situation is to reuse existing multi-purpose equipment, although this comes with performance limitations. Here, a multi-purpose TEM with a side entry cryo-holder was used to evaluate the potential of high-resolution SPA, resulting in a 3 Å resolution map of apoferritin with local resolution extending to 2.6 Å. This map clearly showed two positions of an aromatic side chain. Further, examination of optimal imaging conditions depending on two different multi-purpose electron microscope and camera combinations was carried out, demonstrating that higher magnifications are not always necessary or desirable. Since automation is effectively a requirement for large-scale data collection, and augmenting the multi-purpose equipment is possible, we expanded testing by acquiring data with SerialEM using a β-galactosidase test sample. This study demonstrates the possibilities of more widely available and established electron microscopes, and their applications for cryo-EM SPA.
History
DepositionMar 12, 2020-
Header (metadata) releaseMar 17, 2021-
Map releaseMar 17, 2021-
UpdateMar 17, 2021-
Current statusMar 17, 2021Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.035
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.035
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30100.png

Downloads & links

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Map

FileDownload / File: emd_30100.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3.4A apoferritin, JEM-2100F K2 Summit, 40K, RELION 3, manual acqusition, postprocessed map.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 256 pix.
= 238.08 Å		0.93 Å/pix.
x 256 pix.
= 238.08 Å		0.93 Å/pix.
x 256 pix.
= 238.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.035 / Movie #1: 0.035
Minimum - Maximum-0.077842 - 0.13970813
Average (Standard dev.)-3.1515814e-05 (±0.007945074)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 238.08 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.930.930.93
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z238.080238.080238.080
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0780.140-0.000

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Supplemental data

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Mask #1

Fileemd_30100_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: 3.4A apoferritin, JEM-2100F K2 Summit, 40K, RELION 3,...

Fileemd_30100_half_map_1.map
Annotation3.4A apoferritin, JEM-2100F K2 Summit, 40K, RELION 3, manual acqusition, half map 1.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: 3.4A apoferritin, JEM-2100F K2 Summit, 40K, RELION 3,...

Fileemd_30100_half_map_2.map
Annotation3.4A apoferritin, JEM-2100F K2 Summit, 40K, RELION 3, manual acqusition, half map 2.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Apoferritin, 3.4A, JEM-2100F + K2 Summit, 40K, RELION 3.0

EntireName: Apoferritin, 3.4A, JEM-2100F + K2 Summit, 40K, RELION 3.0
Components
  • Complex: Apoferritin, 3.4A, JEM-2100F + K2 Summit, 40K, RELION 3.0

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Supramolecule #1: Apoferritin, 3.4A, JEM-2100F + K2 Summit, 40K, RELION 3.0

SupramoleculeName: Apoferritin, 3.4A, JEM-2100F + K2 Summit, 40K, RELION 3.0
type: complex / ID: 1 / Parent: 0 / Details: Octahedral symmetry.
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Escherichia coli (E. coli)
Molecular weightTheoretical: 500 KDa

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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

BufferpH: 7
GridModel: Quantifoil R1.2/1.3 / Material: MOLYBDENUM / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeJEOL 2100F
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average exposure time: 5.0 sec. / Average electron dose: 46.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal magnification: 40000
Sample stageSpecimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Cooling holder cryogen: NITROGEN

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4.1.10)
Startup modelType of model: OTHER / Details: Ab initio model generated by cisTEM.
Final reconstructionApplied symmetry - Point group: O (octahedral) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.8) / Number images used: 24904
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0.8)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0.8)
FSC plot (resolution estimation)

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