The largest database of trusted experimental protocols

16 protocols using cf400 cu grid

1

SARS-CoV-2 Spike Protein Visualization

Check if the same lab product or an alternative is used in the 5 most similar protocols
Purified SARS-CoV-2 spike was diluted to a concentration of 0.04 mg/mL using 2 mM Tris pH 8.0, 200 mM NaCl and 0.02% NaN3 before being applied to a plasma cleaned CF400-Cu grid (Electron Microscopy Sciences). Protein was then stained using methylamine tungstate (Nanoprobes) before being allowed to dry at room temperature for 15 minutes. This grid was imaged in a Talos TEM (Thermo Fisher Scientific) equipped with a Ceta 16M detector. Micrographs were collected using TIA v4.14 software at a nominal magnification of 92,000×, corresponding to a calibrated pixel size of 1.63 Å/pix. CTF estimation, particle picking and 2D class averaging were performed using cisTEM39 .
+ Open protocol
+ Expand
2

Structural Analysis of Deglycosylated gB-Fab Complex

Check if the same lab product or an alternative is used in the 5 most similar protocols
The postfusion gB was deglycosylated by digestion with Endo H (10% w/w) for 12 hours at 4°C and purified using a Superose6 10/300 column. Deglycosylated gB was mixed with a molar excess of 3–25 Fab and run over a Superose6 10/300 column (GE Healthcare) using 2 mM Tris pH 8.0, 200 mM NaCl, 0.02% NaN3. A CF400-Cu grid (Electron Microscopy Sciences) was plasma cleaned for 30 seconds in a Solarus 950 (Gatan) using a 4:1 mixture of O2 to H2. The purified complex was diluted to a concentration of 0.025 mg/mL and mixed with additional 3–25 Fab to fully saturate the gB trimer before being deposited onto the prepared grid. Micrographs were collected using a 200 kV Talos transmission electron microscope (Thermo Fisher) equipped with a Ceta 16M detector (Thermo Fisher) at a magnification of 92,000×, corresponding to a calibrated pixel size of 1.63 Å. Data were collected manually using TIA v4.14 (Thermo Fisher) at a defocus range of 1.8 to 3.1 μm. CTF-estimation, particle picking and preliminary 2D classification were performed using cisTEM [63 (link)] before particles were exported into cryoSPARC v2.9.0 [64 (link)] for ab initio model generation and 3D classification.
+ Open protocol
+ Expand
3

Structural Analysis of Prefusion hMPV-F:Fab Complex

Check if the same lab product or an alternative is used in the 5 most similar protocols
Postfusion hMPV F was heat-treated at 70 °C for 10 min, then applied to a CF-400-Cu grid (Electron Microscopy Sciences) that had been plasma cleaned for 45 s in a Solarus 950 plasma cleaner (Gatan) with a 4:1 ratio of O2/H2. The grid was stained using methylamine tungstate (Nanoprobes). Prefusion-stabilized hMPV F DS-CavEs2 was incubated with a two-fold molar excess of MPE8 Fab in 1× PBS at room temperature for 30 min. The hMPV-F:Fab complexes were diluted to a concentration of 0.03 mg/mL in 2 mM Tris pH 8.0, 200 mM NaCl and 0.02% NaN3, then deposited on a CF-400-Cu grid. Grids were imaged at a magnification of 92,000× (corresponding to a calibrated pixel size of 1.63 Å/pix) in a Talos F200C TEM microscope equipped with a Ceta 16 M detector (Thermo Fisher Scientific). CTF-estimation and particle picking were performed in cisTEM35 . Particles were then exported to cryoSPARC v2.15.0 for 2D classification36 (link).
+ Open protocol
+ Expand
4

Visualizing SARS-CoV-2 Spike Protein Variants

Check if the same lab product or an alternative is used in the 5 most similar protocols
Purified SARS-CoV-2 S variants were diluted to a concentration of 0.04 mg/mL in 2 mM Tris pH 8.0, 200 mM NaCl and 0.02% NaN3. Each protein was deposited on a CF-400-CU grid (Electron Microscopy Sciences) that had been plasma cleaned for 30 seconds in a Solarus 950 plasma cleaner (Gatan) with a 4:1 ratio of O2/H2 and stained using methylamine tungstate (Nanoprobes). Grids were imaged at a magnification of 92,000X (corresponding to a calibrated pixel size of 1.63 Å/pix) in a Talos F200C TEM microscope equipped with a Ceta 16M detector (Thermo Fisher). Stability experiments with S-2P and HexaPro were performed by imaging samples as described above after 3 rounds of snap freezing with liquid nitrogen and thawing, after storing samples at room temperature for 1–2 days, or after incubating at 50 °C, 55 °C, or 60 °C for 30 minutes in a thermal cycler.
+ Open protocol
+ Expand
5

Negative-Stain Electron Microscopy of GPC/Antibody Complexes

Check if the same lab product or an alternative is used in the 5 most similar protocols
For each GPC/antibody complex, 4 μL of sample (about 0.02 mg/mL) was applied to a CF400-Cu grid (Electron Microscopy Sciences), and stained with 0.75% lab-made uranyl formate (Electron Microscopy Sciences) solution. NS-EM micrographs were collected with a Titan Halo electron microscope (Thermo Fisher Scientific) and a Falcon 3EC direct electron detector at the magnification of 58,000×. 2D average images and NS-EM reconstructions were obtained with either cisTEM (53 ) or CryoSPARC (54 (link)). NS-maps were aligned and displayed using Chimera X (55 (link)).
+ Open protocol
+ Expand
6

Characterizing mAb N3-1 Binding to SARS-CoV-2 Spike

Check if the same lab product or an alternative is used in the 5 most similar protocols
To investigate mAb N3–1 binding to spike proteins, purified SARS-CoV-2 Wuhan-Hu-1 S-HexaPro was incubated with 1.2-fold molar excess of IgG N3–1 in 2 mM Tris pH 8.0, 200 mM NaCl and 0.02% NaN3 on ice for 10 min. The spike-IgG complexes were at a concentration of 0.05 mg/mL in 2 mM Tris pH 8.0, 200 mM NaCl and 0.02% NaN3 prior to deposition on a CF-400-CU grid (Electron Microscopy Sciences) that was plasma cleaned for 30 sec in a Solarus 950 plasma cleaner (Gatan) with a 4:1 ratio of O2/H2 and stained using methylamine tungstate (Nanoprobes). Grids were imaged at a magnification of 92,000X (corresponding to a calibrated pixel size of 1.63 Å/pix) in a Talos F200C TEM microscope equipped with a Ceta 16M detector. The CTF-estimation, particle picking and 2D classification were all performed in cisTEM44 .
+ Open protocol
+ Expand
7

Structural Analysis of S-Fab Complexes

Check if the same lab product or an alternative is used in the 5 most similar protocols
Purified MERS-CoV S-2P or SARS-CoV-2 S-HexaPro were incubated with 2-fold molar excess of Fab22 or Fab72 or Fab20 in 2 mM Tris pH 8.0, 200 mM NaCl and 0.02% NaN3 at room temperature for 30 min. The S-Fab complexes were diluted to a concentration of 0.06 mg/mL in 2 mM Tris pH 8.0, 200 mM NaCl and 0.02% NaN3. Each protein complex was deposited on a CF-400-CU grid (Electron Microscopy Sciences) that had been plasma cleaned for 30 s in a Solarus 950 plasma cleaner (Gatan) with a 4:1 ratio of O2/H2 and stained using methylamine tungstate (Nanoprobes). Grids were imaged at a magnification of 92,000X (corresponding to a calibrated pixel size of 1.63 Å/pix) in a Talos F200C TEM microscope equipped with a Ceta 16M detector (Thermo Fisher Scientific). The CTF-estimation and particle picking were performed in cisTEM (Grant et al., 2018). Particles were then imported into cryoSPARC v2.15.0 for 2D classification (Punjani et al., 2017).
+ Open protocol
+ Expand
8

Negative-Stain EM Visualization of PEDV

Check if the same lab product or an alternative is used in the 5 most similar protocols
PEDV S PC177 was deposited onto a plasma-cleaned CF400-Cu grid (Electron Microscopy Sciences) at a concentration of 0.035 mg/ml before being stained with methylamine tungstate (Nanoprobes). The stained grid was imaged using an FEI Talos transmission electron microscope equipped with a Ceta 16M detector. Micrographs were collected manually using TIA v4.14 at a nominal magnification of ×92,000, corresponding to a calibrated pixel size of 1.63 Å/pixel. A full description of the negative-stain EM data collection parameters can be found in Table 1. CTF estimation, particle picking, 2D classification, ab initio 3D reconstruction, and 3D refinement and sharpening were all performed in cisTEM.
+ Open protocol
+ Expand
9

Structural Characterization of SARS-CoV-2 Spike

Check if the same lab product or an alternative is used in the 5 most similar protocols
Purified 2019-nCoV S was diluted to a concentration of 0.032 mg/mL in 2 mM Tris pH 8.0, 200 mM NaCl and 0.02% NaN3. Diluted S protein was mixed with a 1.5-fold molar excess of ACE2 and the mixture was incubated on ice for 1 minute before 4.8 uL of the protein mixture was deposited on a CF400-Cu grid (Electron Microscopy Sciences) before being stained with methylamine tungstate (Nanoprobes). This grid was imaged in an FEI Talos TEM (Thermo Scientific) equipped with a Ceta 16M detector. Micrographs were collected manually using TIA v4.14 software at a magnification of x92,000, corresponding to a pixel size of 1.63 Å/pixel. CTF estimation, particle picking and 2D class averaging were performed in cisTEM (38 ).
+ Open protocol
+ Expand
10

TEM Imaging of Nanoparticles

Check if the same lab product or an alternative is used in the 5 most similar protocols
For TEM imaging, 2 μl of particles (20 mg/ml) was applied on a CF400-CU grid (Electron Microscopy Sciences) for 1 min. Extra liquid was carefully removed, and the grid was stained by one drop of NANO-W (Nanoprobes) for 1 min. Liquid was removed, and the sample was air-dried before imaging. Images were obtained using Tecnai Osiris (FEI).
+ Open protocol
+ Expand

About PubCompare

Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.

We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.

However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.

Ready to get started?

Sign up for free.
Registration takes 20 seconds.
Available from any computer
No download required

Sign up now

Revolutionizing how scientists
search and build protocols!