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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-22754 | |||||||||
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Title | Aldolase, rabbit muscle (no beam-tilt refinement) | |||||||||
![]() | Aldolase, rabbit muscle (no beam-tilt refinement) | |||||||||
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![]() | glycolysis / gluconeogenesis / Carbohydrate degradation / Homotetramer / LYASE | |||||||||
Function / homology | ![]() 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 | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.9 Å | |||||||||
![]() | Cianfrocco MA / Kearns SE | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 96.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 11.8 KB 11.8 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 10.7 KB | Display | ![]() |
Images | ![]() | 74.1 KB | ||
Filedesc metadata | ![]() | 5.8 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7k9lMC ![]() 7k9xC ![]() 7ka2C ![]() 7ka3C ![]() 7ka4C M: atomic model generated by this map C: citing same article ( |
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Similar structure data | |
EM raw data | ![]() Data size: 87.6 Data #1: Unaligned micrographs of aldolase collected with beam-tilt at 200 kV [micrographs - single frame]) |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Aldolase, rabbit muscle (no beam-tilt refinement) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.91 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Homotetramer of aldolase
Entire | Name: Homotetramer of aldolase |
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Components |
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-Supramolecule #1: Homotetramer of aldolase
Supramolecule | Name: Homotetramer of aldolase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 157 kDa/nm |
-Macromolecule #1: Fructose-bisphosphate aldolase A
Macromolecule | Name: Fructose-bisphosphate aldolase A / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: fructose-bisphosphate aldolase |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 39.263672 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: 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 |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 1.6 mg/mL | ||||||
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Buffer | pH: 7.5 / Component:
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Grid | Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 | ||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV | ||||||
Details | Pure 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
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: GATAN K2 BASE (4k x 4k) / Average exposure time: 10.0 sec. / Average electron dose: 42.0 e/Å2 Details: Images were collected on a Talos Arctica transmission electron microscope (Thermo Fisher) operating at 200 keV with a gun lens of 6, a spot size of 6, 70 um C2 aperture and 100 um objective ...Details: Images were collected on a Talos Arctica transmission electron microscope (Thermo Fisher) operating at 200 keV with a gun lens of 6, a spot size of 6, 70 um C2 aperture and 100 um objective aperture using beam-image shift. Movies were collected using a K2 direct electron detector (Gatan Inc.) operating in counting mode at 45,000x corresponding to a physical pixel size of 0.91 A/pixel with a 10 sec exposure using 200 ms per frame. Using an exposure rate of 4.204 e/pix/sec, each movie had a total dose of approximately 42 e/A2 for the 2,111 movies over a defocus 0.8-2 um. |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 0.002 µm / Nominal defocus min: 0.0008 µm / Nominal magnification: 45000 |
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |