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- EMDB-20213: The cryo-EM structure of Jack bean urease: further beyond the phy... -

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Basic information

Entry
Database: EMDB / ID: EMD-20213
TitleThe cryo-EM structure of Jack bean urease: further beyond the physical Nyquist limit using the K3 detector
Map dataJack bean urease
Sample
  • Complex: Jack bean urease
Biological speciesCanavalia ensiformis (jack bean)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.06 Å
AuthorsFeathers JR / Spoth KA / Fromme JC
Funding support United States, 1 items
OrganizationGrant numberCountry
National Science Foundation (United States)DMR-1719875 United States
CitationJournal: J Struct Biol X / Year: 2021
Title: Experimental evaluation of super-resolution imaging and magnification choice in single-particle cryo-EM.
Authors: J Ryan Feathers / Katherine A Spoth / J Christopher Fromme /
Abstract: The resolution of cryo-EM reconstructions is fundamentally limited by the Nyquist frequency, which is half the sampling frequency of the detector and depends upon the magnification used. In ...The resolution of cryo-EM reconstructions is fundamentally limited by the Nyquist frequency, which is half the sampling frequency of the detector and depends upon the magnification used. In principle, super-resolution imaging should enable reconstructions to surpass the physical Nyquist limit by increasing sampling frequency, yet there are few reports of reconstructions that do so. Here we directly examine the contribution of super-resolution information, obtained with the K3 direct electron detector using a 2-condenser microscope, to single-particle cryo-EM reconstructions surpassing the physical Nyquist limit. We also present a comparative analysis of a sample imaged at four different magnifications. This analysis demonstrates that lower magnifications can be beneficial, despite the loss of higher resolution signal, due to the increased number of particle images obtained. To highlight the potential utility of lower magnification data collection, we produced a 3.5 Å reconstruction of jack bean urease with particles from a single micrograph.
History
DepositionMay 8, 2019-
Header (metadata) releaseJun 26, 2019-
Map releaseJun 3, 2020-
UpdateApr 21, 2021-
Current statusApr 21, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0256
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0256
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20213.png

Downloads & links

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Map

FileDownload / File: emd_20213.map.gz / Format: CCP4 / Size: 38.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationJack bean urease
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 216 pix.
= 226.8 Å		1.05 Å/pix.
x 216 pix.
= 226.8 Å		1.05 Å/pix.
x 216 pix.
= 226.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0256 / Movie #1: 0.0256
Minimum - Maximum-0.16598174 - 0.25755918
Average (Standard dev.)0.0004937553 (±0.011697096)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions216216216
Spacing216216216
CellA=B=C: 226.79999 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.051.051.05
M x/y/z216216216
origin x/y/z0.0000.0000.000
length x/y/z226.800226.800226.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS216216216
D min/max/mean-0.1660.2580.000

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Supplemental data

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Additional map: Jack bean urease, additional map

Fileemd_20213_additional.map
AnnotationJack bean urease, additional map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Jack bean urease, additional map

Fileemd_20213_additional_1.map
AnnotationJack bean urease, additional map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Jack bean urease, half map #1

Fileemd_20213_half_map_1.map
AnnotationJack bean urease, half map #1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Jack bean urease, half map #2

Fileemd_20213_half_map_2.map
AnnotationJack bean urease, 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 : Jack bean urease

EntireName: Jack bean urease
Components
  • Complex: Jack bean urease

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Supramolecule #1: Jack bean urease

SupramoleculeName: Jack bean urease / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Canavalia ensiformis (jack bean)
Molecular weightTheoretical: 550 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

Concentration1 mg/mL
BufferpH: 7.4
GridDetails: unspecified
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TECNAI ARCTICA
Specialist opticsEnergy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 39.93 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 39000
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

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3la4

Final reconstructionApplied symmetry - Point group: D3 (2x3 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 3.06 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 111111
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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