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- PDB-7k9l: Aldolase, rabbit muscle (no beam-tilt refinement) -

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Basic information

Entry
Database: PDB / ID: 7k9l
TitleAldolase, rabbit muscle (no beam-tilt refinement)
ComponentsFructose-bisphosphate aldolase A
KeywordsLYASE / glycolysis / gluconeogenesis / Carbohydrate degradation / Homotetramer
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.9 Å
AuthorsCianfrocco, M.A. / Kearns, S.E. / Cash, J.N. / Li, Y.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1759826 United States
National Institutes of Health/Office of the DirectorS10OD020011 United States
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, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
B: Fructose-bisphosphate aldolase A
A: Fructose-bisphosphate aldolase A
C: Fructose-bisphosphate aldolase A
D: Fructose-bisphosphate aldolase A


Theoretical massNumber of molelcules
Total (without water)157,0554
Polymers157,0554
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Fructose-bisphosphate aldolase A / Muscle-type aldolase


Mass: 39263.672 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: ALDOA / Production host: Oryctolagus cuniculus (rabbit) / Tissue (production host): Muscle / References: UniProt: P00883, fructose-bisphosphate aldolase

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Homotetramer of aldolase / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightValue: 157 kDa/nm / Experimental value: YES
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameBuffer-ID
120 mMHEPES1
250 mMNaCl1
SpecimenConc.: 1.6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
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 ...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.
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal magnification: 45000 X / Nominal defocus max: 2 nm / Nominal defocus min: 0.8 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm
Image recordingAverage exposure time: 10 sec. / Electron dose: 42 e/Å2 / Film or detector model: GATAN K2 BASE (4k x 4k)
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.

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Processing

SoftwareName: PHENIX / Version: 1.14_3260: / Classification: refinement
EM software
IDNameVersionCategory
1Warpparticle selection
4CTFFIND4CTF correction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 718578
3D reconstructionResolution: 4.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 186471 / Symmetry type: POINT

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