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- EMDB-22756: Aldolase, rabbit muscle (beam-tilt refinement x2) -

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Basic information

Entry
Database: EMDB / ID: EMD-22756
TitleAldolase, rabbit muscle (beam-tilt refinement x2)
Map dataAldolase, rabbit muscle (beam-tilt refinement x2)
Sample
  • Complex: Homotetramer of aldolase
    • Protein or peptide: Fructose-bisphosphate aldolase A
Keywordsglycolysis / gluconeogenesis / carbohydrate degradation / homotetramer / LYASE
Function / homology
Function and homology information


negative regulation of Arp2/3 complex-mediated actin nucleation / fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / M band / I band / fructose 1,6-bisphosphate metabolic process / glycolytic process / protein homotetramerization / positive regulation of cell migration / cytosol
Similarity search - Function
Fructose-bisphosphate aldolase class-I active site / Fructose-bisphosphate aldolase class-I active site. / Fructose-bisphosphate aldolase, class-I / Fructose-bisphosphate aldolase class-I / Aldolase-type TIM barrel
Similarity search - Domain/homology
Fructose-bisphosphate aldolase A
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsKearns SK / Cash JN
Funding support2 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1759826
National Institutes of Health/Office of the DirectorS10OD020011
CitationJournal: IUCrJ / Year: 2020
Title: High-resolution cryo-EM using beam-image shift at 200 keV.
Authors: Jennifer N Cash / Sarah Kearns / Yilai Li / Michael A Cianfrocco /
Abstract: Recent advances in single-particle cryo-electron microscopy (cryo-EM) data collection utilize beam-image shift to improve throughput. Despite implementation on 300 keV cryo-EM instruments, it ...Recent advances in single-particle cryo-electron microscopy (cryo-EM) data collection utilize beam-image shift to improve throughput. Despite implementation on 300 keV cryo-EM instruments, it remains unknown how well beam-image-shift data collection affects data quality on 200 keV instruments and the extent to which aberrations can be computationally corrected. To test this, a cryo-EM data set for aldolase was collected at 200 keV using beam-image shift and analyzed. This analysis shows that the instrument beam tilt and particle motion initially limited the resolution to 4.9 Å. After particle polishing and iterative rounds of aberration correction in , a 2.8 Å resolution structure could be obtained. This analysis demonstrates that software correction of microscope aberrations can provide a significant improvement in resolution at 200 keV.
History
DepositionSep 29, 2020-
Header (metadata) releaseDec 2, 2020-
Map releaseDec 2, 2020-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0212
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0212
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7ka2
  • Surface level: 0.0212
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22756.png

Downloads & links

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Map

FileDownload / File: emd_22756.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAldolase, rabbit muscle (beam-tilt refinement x2)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.91 Å/pix.
x 300 pix.
= 273. Å		0.91 Å/pix.
x 300 pix.
= 273. Å		0.91 Å/pix.
x 300 pix.
= 273. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.91 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0212 / Movie #1: 0.0212
Minimum - Maximum-0.03234312 - 0.06923036
Average (Standard dev.)0.0000014275214 (±0.0020864394)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 273.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.910.910.91
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z273.000273.000273.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ360360360
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.0320.0690.000

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Supplemental data

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Sample components

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Entire : Homotetramer of aldolase

EntireName: Homotetramer of aldolase
Components
  • Complex: Homotetramer of aldolase
    • Protein or peptide: Fructose-bisphosphate aldolase A

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Supramolecule #1: Homotetramer of aldolase

SupramoleculeName: Homotetramer of aldolase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 157 kDa/nm

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Macromolecule #1: Fructose-bisphosphate aldolase A

MacromoleculeName: Fructose-bisphosphate aldolase A / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: fructose-bisphosphate aldolase
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 39.263672 KDa
Recombinant expressionOrganism: Oryctolagus cuniculus (rabbit)
SequenceString: PHSHPALTPE QKKELSDIAH RIVAPGKGIL AADESTGSIA KRLQSIGTEN TEENRRFYRQ LLLTADDRVN PCIGGVILFH ETLYQKADD GRPFPQVIKS KGGVVGIKVD KGVVPLAGTN GETTTQGLDG LSERCAQYKK DGADFAKWRC VLKIGEHTPS A LAIMENAN ...String:
PHSHPALTPE QKKELSDIAH RIVAPGKGIL AADESTGSIA KRLQSIGTEN TEENRRFYRQ LLLTADDRVN PCIGGVILFH ETLYQKADD GRPFPQVIKS KGGVVGIKVD KGVVPLAGTN GETTTQGLDG LSERCAQYKK DGADFAKWRC VLKIGEHTPS A LAIMENAN VLARYASICQ QNGIVPIVEP EILPDGDHDL KRCQYVTEKV LAAVYKALSD HHIYLEGTLL KPNMVTPGHA CT QKYSHEE IAMATVTALR RTVPPAVTGV TFLSGGQSEE EASINLNAIN KCPLLKPWAL TFSYGRALQA SALKAWGGKK ENL KAAQEE YVKRALANSL ACQGKYTPSG QAGAAASESL FISNHAY

UniProtKB: Fructose-bisphosphate aldolase A

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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

Concentration1.6 mg/mL
BufferpH: 7.5 / Component:
ConcentrationName
20.0 mMHEPES
50.0 mMNaCl
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
DetailsPure aldolase isolated from rabbit muscle was purchased as a lyophilized powder (Sigma Aldrich) and solubilized in 20 mM HEPES (pH 7.5), 50 mM NaCl at 1.6 mg/ml. Sample was blotted for 4 seconds with Whatman No. #1 filter paper immediately prior to plunge freezing in liquid ethane cooled by liquid nitrogen.

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 42.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated magnification: 4500 / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 0.002 µm / Nominal defocus min: 0.0008 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 718578
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5vy5

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 186841
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
FSC plot (resolution estimation)

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