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- EMDB-20016: The cryo-EM structure of Jack bean urease: beyond the physical Ny... -

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Basic information

Entry
Database: EMDB / ID: EMD-20016
TitleThe cryo-EM structure of Jack bean urease: beyond the physical Nyquist limit using the K3 detector
Map dataJack bean urease
Sample
  • Complex: Jack bean urease
Function / homology
Function and homology information


urease complex / urease / urease activity / urea catabolic process / : / nickel cation binding / toxin activity
Similarity search - Function
Urease / Urease subunit beta-alpha, linker domain / Urease subunit beta-alpha linker domain / Urease active site / Urease active site. / Urease nickel binding site / Urease nickel ligands signature. / Urease, beta subunit / Urease, alpha subunit / Urease alpha subunit, C-terminal ...Urease / Urease subunit beta-alpha, linker domain / Urease subunit beta-alpha linker domain / Urease active site / Urease active site. / Urease nickel binding site / Urease nickel ligands signature. / Urease, beta subunit / Urease, alpha subunit / Urease alpha subunit, C-terminal / Urease, beta subunit superfamily / Urease beta subunit / Urease domain profile. / Urease alpha-subunit, N-terminal domain / Urease alpha-subunit, N-terminal domain / Urease, gamma/gamma-beta subunit / Urease, gamma subunit superfamily / Urease, gamma subunit / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolase
Similarity search - Domain/homology
Biological speciesCanavalia ensiformis (jack bean)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.77 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
DepositionMar 22, 2019-
Header (metadata) releaseMay 1, 2019-
Map releaseMar 25, 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: 0.015
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7kns
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20016.png

Downloads & links

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Map

FileDownload / File: emd_20016.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationJack bean urease
Voxel sizeX=Y=Z: 0.83 Å
Density
Contour LevelBy AUTHOR: 0.015 / Movie #1: 0.015
Minimum - Maximum-0.06541672 - 0.10846457
Average (Standard dev.)0.000101086676 (±0.0034292187)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 318.72 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.830.830.83
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z318.720318.720318.720
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-0.0650.1080.000

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Supplemental data

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Half map: Jack bean urease, half map #1

Fileemd_20016_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_20016_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
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TECNAI ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 49000
Specialist opticsEnergy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 44.0 e/Å2
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

Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionApplied symmetry - Point group: D3 (2x3 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 2.77 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 56038
FSC plot (resolution estimation)

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