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In This Article

  • Summary
  • Abstract
  • Introduction
  • Protocol
  • Results
  • Discussion
  • Disclosures
  • Acknowledgements
  • Materials
  • References
  • Reprints and Permissions

Summary

This protocol describes techniques used to determine ion channel structures by cryo-electron microscopy, including a baculovirus system used to efficiently express genes in mammalian cells with minimum effort and toxicity, protein extraction, purification, and quality checking, sample grid preparation and screening, as well as data collection and processing.

Abstract

Transient receptor potential channels (TRPCs) of the canonical TRP subfamily are nonselective cation channels that play an essential role in calcium homeostasis, particularly store-operated calcium entry, which is critical to maintaining proper function of synaptic vesicle release and intracellular signaling pathways. Accordingly, TRPC channels have been implicated in a variety of human diseases including cardiovascular disorders such as cardiac hypertrophy, neurodegenerative disorders such as Parkinson's disease, and neurologic disorders such as spinocerebellar ataxia. Therefore, TRPC channels represent a potential pharmacologic target in human diseases. However, the molecular mechanisms of gating in these channels are still unclear. The difficulty in obtaining large quantities of stable, homogeneous, and purified protein has been a limiting factor in structure determination studies, particularly for mammalian membrane proteins such as the TRPC ion channels. Here, we present a protocol for the large-scale expression of mammalian ion channel membrane proteins using a modified baculovirus gene transfer system and the purification of these proteins by affinity and size-exclusion chromatography. We further present a protocol to collect single-particle cryo-electron microscopy images from purified protein and to use these images to determine the protein structure. Structure determination is a powerful method for understanding the mechanisms of gating and function in ion channels.

Introduction

Calcium is involved in most cellular processes including signaling cascades, transcription control, neurotransmitter release, and hormone molecule synthesis1,2,3. The homeostatic maintenance of cytosolic free calcium is crucial to the health and function of cells. One of the major mechanisms of intracellular calcium homeostasis is store-operated calcium entry (SOCE), a process in which depletion of calcium stored in the endoplasmic reticulum (ER) triggers the opening of ion channels on the plasma membrane to facilitate the replenishment of ER calcium, which can then be used in further signaling4,5,6. Transient receptor potential channels (TRPCs), which are calcium-permeable channels belonging to the TRP superfamily, have been identified as a major participant in SOCE7,8,9 .

Among the seven members in the TRPC family, TRPC3, TRPC6, and TRPC7 form a homologue subgroup, and they are unique in the ability to be activated by the lipid secondary messenger diacylglycerol (DAG), a degradation product of the signaling lipid phosphatidylinositol 4,5-bisphosphate (PIP2)10,11. TRPC3 is highly expressed in smooth muscle and in the cerebral and cerebellar regions of the brain, where it plays essential roles in calcium signaling that impact neurotransmission and neurogenesis12,13. Dysfunction of TRPC3 has been linked to central nervous system disorders, cardiovascular disorders, and certain cancers such as ovarian adenocarcinoma14,15,16. Therefore, TRPC3 holds promise as a pharmaceutical target for treatment of these diseases. The development of specifically targeted drugs acting on TRPC3 has been limited by a lack of understanding of its molecular activation mechanisms, including lipid binding sites17,18. We have reported the first atomic-resolution structure of the human TRPC3 channel (hTRPC3) and its two lipid binding sites in a closed state, providing important insights into these mechanisms19.

The key factor for determining the structure of a membrane protein at high resolution is to obtain protein of high quality. The corresponding screening of expression and purification conditions necessary to obtain high quality protein can be a time-consuming and costly endeavor. Here we present a protocol describing in detail how we identify the optimal conditions for the expression and purification of hTRPC3, which behaved poorly in our initial screening. We present several key points on how to troubleshoot and optimize the protein behavior, which lay a solid foundation for our cryo-electron microscopy (cryo-EM) studies. We use a modified baculoviral generating vector (pEG), developed by Gouaux and colleagues, which is optimized for screening assays and efficient generation of baculovirus in mammalian cells20. This expression method is appropriate for rapid and cost-effective overexpression of proteins in the mammalian cell membrane. We combine the use of this vector with a fluorescence-detection size-exclusion chromatography-based (FSEC) prescreening method21. This method uses a green fluorescent protein (GFP) tag fused to the construct of interest and improves visualization of the target protein in small, whole-cell solubilized samples. This allows for screening of protein stability in the presence of different detergents and additives, with thermostabilizing mutations, and allows the use of a small number of cells from small-scale transient transfection. In this way, a multitude of conditions can be rapidly screened before moving to a large-scale protein purification. Following expression, screening, and purification, we present a protocol for obtaining and processing images from cryo-EM to generate a de novo structural determination of the protein. We believe that the approaches described here will serve as a generalizable protocol for structural studies of TRP channel receptors and other membrane proteins.

Protocol

1. Transformation of DH10α Competent Cells to Produce Bacmid DNA

  1. Synthesize the gene of interest and subclone it into a modified version of the pEG vector containing a twin strep-tag, a His8-tag, and GFP with a thrombin cleavage site at the N terminus (pFastBacI)20.
  2. Transform competent cells by adding 5 ng of plasmid containing a desired gene in pFastBacI to 50 μL of DH10α cells in a 1.5 mL tube and incubate for 10 min on ice. Heat shock the cells for 45 s at 42 °C. Add 200 μL of super optimal broth with catabolic repressor (SOC) medium to the tube and incubate for 4 - 8 h at 37 °C in an orbital shaker at 225 rpm.
  3. Plate 5 μL of cells on a bacmid LB agar plate (50 μg/mL kanamycin, 7 μg/mL gentamicin, 10 μg/mL tetracycline, 100 μg/mL Bluo-gal, and 40 μg/mL isopropyl β-D-1-thiogalactopyranoside [IPTG], agar).
  4. Incubate the plate for 48 h at 37 °C.
    NOTE: The Bluo-gal indicator stains colonies that are still expressing lacZ (vector insertion unsuccessful), allowing for selection of white (successfully transformed) colonies.
  5. Carefully select an isolated white colony, avoiding any white colonies that are in contact with blue colonies, and grow cells overnight in 6 mL of bacmid LB medium (50 μg/mL kanamycin, 7 μg/mL gentamicin, 10 μg/mL tetracycline) at 37 °C in an orbital shaker at 225 rpm.

2. Bacterial Preparation for Isolation of Bacmid DNA

  1. To isolate bacmid DNA, spin down Escherichia coli cells for 10 min at 2880 x g.
  2. Discard the supernatant and resuspend the pellet in 200 µL of cell resuspension solution from the miniprep kit (see Table of Materials) by pipetting. Be sure the pellet is fully and homogenously suspended. Then, transfer the cell suspension into 1.5 mL tubes.
  3. Add 200 µL of the cell lysis solution from the miniprep kit and mix by inverting the tube a few times. Incubate for up to 5 min at room temperature (RT) to lyse the cells. Add 200 µL of neutralization solution from the miniprep kit and mix by inverting tube a few times to stop the lysis reaction.
  4. Spin down for 10 min at 21,130 x g in a table-top centrifuge. Collect 600 μL of supernatant in a 2 mL tube. Add 600 μL phenol:chloroform:isoamyl alcohol solution (see Table of Materials) and mix thoroughly to extract the DNA from the remainder of the cell lysis products.
    CAUTION: Phenol:chloroform:isoamyl alcohol solution is toxic by inhalation, in contact with skin, and if swallowed. It can cause chemical burns and may be carcinogenic. Wear gloves and a buttoned lab coat. Work in a fume hood. Dispose of this hazardous waste appropriately.
  5. Spin the tube for 10 min at 21130 x g in a table-top centrifuge. Two separate liquid phases will be visible. Carefully transfer 300 μL of the upper aqueous phase to a new tube. Add 600 μL of 100% ethanol to wash the DNA. Gently invert the tube to mix.
    NOTE: Do not vortex, as this can shear bacmid DNA.
  6. Cool tubes by placing them in a -20 °C freezer for 10 min. Spin down for 10 min at 21,130 x g in a table-top centrifuge. Discard the supernatant and preserve the DNA pellet.
  7. Add 1 mL of 70% ethanol to wash the pellet. Gently invert the tube to mix. Spin for 10 min at 21,130 x g in a table top centrifuge. Discard the supernatant and allow the pellet to air dry for approximately 5 min or until no liquid is visible in the tube and the DNA pellet becomes translucent.
  8. Resuspend the dry pellet in 50 µL of sterile, DNase-free, deionized water. Measure the DNA concentration.
    NOTE: Do not freeze bacmid DNA. Store at 4 °C for up to several days.

3. Transfection of Sf9 Insect Cells with Bacmid to Produce P1 Baculovirus

  1. Seed 0.9 x 106 Sf9 cells/well in 2 mL of appropriate medium (see Table of Materials) in each well of a 6-well tissue culture plate. Incubate cells at 27 °C for 20 min to promote attachment to the plate.
    CAUTION: Cell cultures are a potential biohazard. Work in an approved laminar flow hood using aseptic techniques and check institutional and governmental guidelines for recommended protective clothing and proper disposal of waste prior to performing experiments.
  2. After attachment, add 8 µL of transfection reagent (see Table of Materials) to 100 µL of media for each well of the 6 well plate being transfected in a sterile tube. Add 6 μg of bacmid DNA to 100 µL of medium in a separate sterile tube. Incubate 5 min at RT. Combine the two solutions and incubate for 45 min at RT.
  3. Replace the medium in the 6 wells with 2 mL of fresh medium. Add the mixture from previous step to each well dropwise (200 µL per well). Gently rock the plate to ensure mixing of the transfection solution into the medium.
    NOTE: Do not swirl or shake the plate because this will cause cells to detach.
  4. Incubate cells for 5 d (120 h) in a 27 °C humidified incubator. Check GFP fluorescence before harvesting to verify that virus is being produced in a large percentage of cells; if the percentage is low, extend the incubation time as necessary (see Figure 1C).
  5. Collect the supernatant containing P1 virus (about 2 mL from each well). Filter the medium containing P1 virus into 2-mL tubes using a 3 mL syringe and small 0.2 µm filter. Add sterile fetal bovine serum (FBS) to a final concentration of 1%.
    NOTE: This stock of P1 virus should be stored at 4 °C and be protected from light.

4. Infection of Sf9 Insect Cells with P1 Baculovirus to Produce P2 Baculovirus

  1. Prepare 200 mL (or desired volume) of Sf9 cells at a concentration of 0.8 - 0.9 x 106 cells/mL in appropriate medium (see Table of Materials) in a flat bottom Erlenmeyer culture flask of sufficient size.
    NOTE: For suspension culture, the volume used should not exceed 40% of the total capacity of the flask.
  2. Add 1:2500 ratio (v/v) of P1 virus stock from 3.5 to the Sf9 cell suspension culture. Incubate for the time of optimal virus expression (usually 48 - 120 h depending on the protein construct) at 27 °C in an orbital shaker at 115 rpm.
    NOTE: The relative virus expression can be determined by viewing the GFP fluorescence of the virus in a sample of the culture.
  3. Centrifuge the cell suspension for 40 min at 11,520 x g and collect the supernatant containing P2 virus. Filter the supernatant using disposable 0.2 µm filters. Add FBS to a final concentration of 0.5%.
    NOTE: This stock of P2 virus should be stored at 4 °C and be protected from light.
  4. Obtain a titer for the P2 virus using Sf9easy cells or a virus counter.

5. Infection of HEK293 Mammalian Cells with P2 Baculovirus for Large-scale Protein Expression

  1. Prepare a desirable volume of HEK293 mammalian cell suspension culture (4 - 6 L is recommended for preparation of frozen grids) at a concentration of 3.5 - 3.8 x 106 cells/mL in the expression medium (see Table of Materials) supplemented with 1% (v/v) sterile FBS in baffled-bottom Erlenmeyer culture flasks of sufficient size.
    NOTE: For suspension culture, the volume used should not exceed 40% of the total volume of the flask.
  2. Add 8% (v/v) of P2 virus stock solution from step 4.3 to the HEK293 cell suspension culture. Incubate at 37 °C in an orbital shaker at 135 rpm.
  3. Add 10 mM sodium butyrate at 12 - 18 h post-infection. Incubate for the time of optimal protein expression (usually 36 - 72 h) at 30 °C.
  4. Harvest cells by centrifuging for 20 min at 2,880 x g. Wash cells by resuspending in approximately 100 mL tris-buffered saline (TBS) per liter of cells harvested. Centrifuge again for 20 min at 2,880 x g and collect the cell pellet.
    NOTE: The protocol may be paused here. Cell pellets can be snap-frozen in liquid nitrogen and stored at -80 °C until purification.
    CAUTION: Liquid nitrogen may cause cryogenic burns or injury. It may cause frostbite. It may displace oxygen and cause rapid suffocation. Wear cold insulating gloves and face shield.
  5. Collect small 1 mL harvests at varying time points and solubilize for 2 h at 4 °C with rocking or stirring in the presence of different detergents and/or additives. These small whole-cell solubilized samples can be clarified by ultracentrifugation at 235,000 × g for 10 min at 4 °C and run as a 30 μL sample on a size-exclusion chromatography (SEC) column (see Table of Materials) to determine the best time for expression and the best solubilization conditions.
    NOTE: In the case of hTRPC3, this screening included different buffers with pH values from 4.0 - 9.5 and salt concentrations of 50 - 500 mM; different ionic compositions (such as MgCl2 or NaCl); different detergents with critical micelle concentration (CMC) values of 0.1 - 20 mM; reducing additives such as dithiothreitol, tris(2-carboxyethyl)phosphine, and β-mercaptoethanol; and the calcium-chelating additive ethylenediaminetetraacetic acid (EDTA).

6. Purification of hTRPC3 Protein from the Frozen Cell Pellet

  1. Thaw the pellet in buffer containing 20 mM Tris (pH 8.0), 500 mM NaCl, 1 mM phenylmethylsulfonyl fluoride (PMSF), 0.8 μM aprotinin, 2 μg/mL leupeptin, 2 mM pepstatin A, and 1% digitonin, using 100 mL of buffer per liter of cells harvested. Once thawed, ensure homogeneity of the solution by pipetting or stirring. Allow to solubilize for 2 h at 4 °C in a beaker immersed in ice with a stir bar rotating.
  2. Remove cell debris by ultracentrifugation at 235,000 × g for 1 h at 4 °C. Verify protein quantity by running a 30 μL sample on an SEC column (see Table of Materials) by high performance liquid chromatography (HPLC) and visualize the target protein by the GFP signal output.
  3. Incubate the solubilized protein (supernatant) with cobalt affinity resin for 1 - 2 h at 4 °C. Verify protein binding to the resin by running a 30 μL sample on an SEC column.
    NOTE: If protein binding has occurred, the GFP tagged protein target will be retained on the column, not found in the flow-through. Therefore, no GFP signal will be present at the position corresponding to the target protein size when the flow-through is run on HPLC.
  4. Wash the resin with 10 column volumes of buffer (20 mM Tris, pH 8.0, 500 mM NaCl, 15 mM imidazole, and 0.1% digitonin). Check for protein loss by running a 30 μL sample on an SEC column.
    NOTE: If protein loss from the column has occurred, the GFP tagged protein target will be found in the wash buffer that has passed over the column. Therefore, GFP signal will be present at the position corresponding to the target protein size when the wash buffer is run on HPLC. If protein loss has occurred, the imidazole concentration of the wash buffer may need to be lowered to prevent disrupting His tag binding to the affinity column.
  5. Elute the resin-bound hTRPC3 with buffer (20 mM Tris, pH 8.0, 500 mM NaCl, 250 mM imidazole, and 0.1% digitonin). Add thrombin at a 1:20 molar ratio (to cleave the GFP tag) and add 10 mM EDTA (an hTRPC3 stabilizing agent) to the eluted sample and incubate for 3 h at 4 °C. Check that protein has been eluted by running 90 μL of a sample diluted 1:100 on an SEC column and verifying the presence of a GFP signal at the position corresponding to the target protein size.
    NOTE: At this point, the tryptophan signal from total protein in the elution can also be viewed. Only the target affinity-purified protein will remain in the elution and the GFP and tryptophan signals will be near identical in profile. If the target protein is not seen in large quantity in the elution but was not lost in the flow-through or wash, the protein has likely remained bound to the column and can be eluted using a higher concentration of imidazole in the buffer.
  6. Concentrate the eluate to 500 μL or less in a 15 mL 100K centrifugal filter tube (see Table of Materials) by spinning at 2,880 x g at 4 °C in 5 min increments. Resuspend the protein by pipetting the solution up and down between spins to avoid overconcentrating.
    NOTE: Centrifuge time may be shortened as the volume approaches the desired final volume.
  7. Load the concentrate onto an SEC column in buffer (20 mM Tris, pH 8.0, 500 mM NaCl, 1 mM EDTA, and 0.1% digitonin). Run .
  8. Combine peak fractions containing the intact TRPC3 tetramer, as visualized by UV absorbance signal, and concentrate again to a final concentration of at least 5 mg/mL.

7. Screening of Protein by Negative-stain Electron Microscopy

  1. Turn on the glow-discharge machine. Set the program for discharging a carbon-coated grid using argon and oxygen for 30 s. Run the program to make the carbon-coating on copper 400-mesh grids hydrophilic prior to addition of the protein solution.
  2. Set up five 40 μL drops of sterile water and two 40 μL drops of 1% uranyl formate solution (on lab film, wax paper, or a similar surface, see Table of Materials). Take the grid from step 7.1 and add 2.5 μL of protein sample 5 mg/mL (50 - 200 μM) onto the dark side and let it sit for 1 min.
  3. After 1 min, dry the grid using filter paper. Do not touch the filter paper directly to the grid surface; instead, bring the paper to the edge of the liquid droplet and allow capillary action to pull the liquid from the grid into the filter paper.
  4. Dip the grid into first drop of water. Dry with filter paper and repeat with the remaining drops of water and the first drop of uranyl formate. Allow the second drop of uranyl formate sit for 1 min and then dry with filter paper. Allow the grid to fully air dry (about 1 min) before storing.
    NOTE: This staining protocol may not be ideal for all protein-detergent combinations. Different concentrations of uranyl formate stain and different lengths of time for stain exposure should be tested if the steps above do not provide a stain with good contrast.
  5. Image the grids on an electron microscope (see Table of Materials) to check the protein particle quality. Ensure that the micrographs show numerous particles that are homogenous in general appearance and distribution, display good contrast, and match the predicted size of the target protein.
  6. Generate preliminary, low-resolution, two-dimensional (2D) classifications using 50 - 100 micrographs (see data processing – step 10) to check that the particles represent different views of a single consistent structure.
    NOTE: Micrographs and preliminary 2D classes of sufficient quality, as described above, are a strong indicator that the protocol has been sufficiently optimized for protein purification. Preparation and screening of cryo-EM grids is warranted at this point.

8. EM Sample Preparation

  1. Glow-discharge a gold holey carbon grid (see Table of Materials) as described in step 7.1.
  2. Apply 2.5 μL of the concentrated hTRPC3 protein sample (5 mg/mL) onto the grid. Blot the grid for 1.5 s using a blot force of 1 and a wait time of 5 s at 100% humidity and 4 °C, then plunge the grid into liquid ethane cooled by liquid nitrogen using a vitrification machine.
    NOTE: The humidity, temperature, blot-force, blot time, and wait time listed here were used for the authors’ hTRPC3 study19. They may need to be changed to produce optimal vitreous ice for other proteins and detergents.
  3. Screen frozen grids for optimal ice conditions using a cryo-EM microscope (see Table of Materials) and manually view regions of thick ice (grid squares that appear smaller and darker), thin ice (grid squares that appear larger and brighter), and medium ice.
    NOTE: Thicker ice often holds more particles, while thinner ice often yields better contrast and resolution. Use manual screening of images to determine which ice conditions results in a large number of monodispersed particles with good contrast and resolution. Once good conditions are verified, move to image collection on a 300 kV cryo-EM microscope.

9. EM Data Collection

  1. Using an automated acquisition program, record image stacks in super-resolution counting mode with a binned pixel size of 1.074 Å on an electron microscope operated at 300 kV with a nominal magnification of 130,000X direct electron detector.
  2. Dose-fractionate every image to 40 frames with a total exposure time of 8 s, with 0.2 s per frame and a dose rate of 6.76 e− Å−2 s−1 (nominal defocus values varied from 1.0 to 2.5 μm in the authors’ experiment).

10. EM Data Processing

  1. Implement motion correction of summed movie stacks22 and estimate defocus values23 using the data processing software (see Table of Materials)24.
  2. Pick particles from the micrographs. Use these picked particles to construct an initial reference-free 2D classification using the software24. Select ideal 2D class averages to use as templates for automated particle picking for the entire data set.
  3. Manually check the quality of the auto-picked particles and remove bad particles. Use multiple rounds of 2D classification to clean up picked particles.
  4. Generate an initial model25. Subject 2D picked particles to three-dimensional (3D) classification (about 5 classes) using C1 symmetry and an initial reconstruction low-pass filter of 60 Å as a reference model. Determine which classes have high-resolution features and combine particles within such a class.
  5. Further refine particles using the local refinement with C4 symmetry (in the case of hTRPC3) applied and a high-resolution limit for particle alignment set to 4.5 Å26.

11. Model Building

  1. Build a model (see Table of Materials for the software used). For hTRPC3, use the transmembrane domain (TMD) of the transient receptor potential melastatin 4 (TRPM4) structure protein data bank (PDB) 5wp6 as a guide27. Use bulky residues and secondary structure prediction to guide de novo building.
  2. Subject the initial model to real space refinement with secondary structure restraints28. Manually examine the refined model and remodify as needed (see Table of Materials for the software used).
  3. Apply Fourier shell correlation (FSC) curves to calculate the difference between the final model and the EM map for validation of the refined structure. Evaluate the geometries of the atomic models (see Table of Materials for the software used)29,30.

Results

A schematic overview of the protocol for expression and purification of hTRPC3 is shown in Figure 1A. An image of the hTRPC3 bacmid plate with ideal white colonies, similar to the one selected for bacmid DNA purification, is shown in Figure 1B. We found that 48 h is ideal for clear Bluo-gal staining while maintaining the presence of isolated colonies. Peak production of P2 virus for hTRPC3, as visualized by GFP fluorescence, was ...

Discussion

Structural determination of proteins by cryo-EM has revolutionized the field of structural biology in the past few years, thanks to the development of new cameras and algorithms that significantly speeds up the structure determination of proteins that do not readily crystalize, particularly membrane proteins. Despite all of the recent advances in the cryo-EM technique, the preparation of purified proteins sufficient in quality and quantity to facilitate high-quality imaging often remains time-consuming, costly, and chall...

Disclosures

The authors have nothing to disclose.

Acknowledgements

We thank G. Zhao and X. Meng for the support with data collection at the David Van Andel Advanced Cryo-Electron Microscopy Suite. We appreciate the VARI High-Performance Computing team for computational support. We give our gratitude to N. Clemente, D. Dues, J. Floramo, Y. Huang, Y. Kim, C. Mueller, B. Roth, and Z. Ruan for comments that greatly improved this manuscript. We thank D. Nadziejka for editorial support for this manuscript. This work was supported by internal VARI funding.

Materials

NameCompanyCatalog NumberComments
pEG BacMam vector (pFastBacI)addgene31488
DH10α cellsLife Technologies10361-012
S.O.C. mediaCorning46003CRfor transformation of DH10α cells for Bacmid
Bacmam culture platesTeknovaL5919for culture of transformed DH10α cells
Incubation shaker for bacterial cellsInfors HTMultitron standard
Incubated orbital shaker for insect cellsThermo-FisherSHKE8000
Reach-in CO2 incubator for mammalian cellsThermo-Fisher3951
Table-top orbital shakerThermo-FisherSHKE416HPused in Reach-in CO2 incubator for mammalian cells
IncubatorVWR1535for bacterial plates
QIAprep Spin Miniprep KitQiagen27106for plasmid extraction and purification
Phenol:Chloroform:Isoamyl alcoholInvitrogen15593031for DNA extraction
Sf9 cellsLife Technologies12659017insect cells for producing virus
Sf-900 mediaGibco12658-027insect cell media
FBSAtlanta BiologicalsS11550
Cellfectin IIGibco10362100for transfecting insect cells
lipofectamine 2000Invitrogen11668-027for transfecting mamalian cells
0.2 mm syringe filterVWR28145-501for filtering P1 virus
0.2 mm filter flasks 500ml resevoirCorning430758for filtering P2 virus
erlenmeyer culture flask (flat bottom 2L)Gene MateF-5909-2000for culturing insect cells
erlenmeyer culture flask (baffled 2L)Gene MateF-5909-2000Bfor culturing mammalian cells
nanodrop 2000 spectrophotometerThermo-FisherND-2000for determining DNA and protein concentrations
HEK293ATCCCRL-3022mammalian cells for producing protein
Freestyle 293 expression MediumGibco1238-018mammalian cell media for protein expression
Butyric Acid Sodium SaltAcros263195000to amplify protein expression
PMSFAcros215740500protease inhibitor
Aprotinin from bovine lungSigma-AldrichA1153-100MGprotease inhibitor
Leupeptin hydrochlorideSigma-Aldrich24125-16-4protease inhibitor
pepstatin AFisher ScientificBP2671-250protease inhibitor
digitoninEMD Millipore300410detergent - to solubilize protein from membrane
imidazoleSigma792527to elute protein from resin column
TALON resinClonetech635504for affinity purification by His-tag
superose6 incease columnsGE29091596; 29091597for HPLC and FPLC
Prominence Modular HPLC SystemShimadzuSee Below
Controller Module"CBM20A
Solvent Delivery System"LC30AD
Fluorescence Detector"RF20AXS
Autosampler with Cooling"SIL20ACHT
Pure FPLC System with FractionatorAkta
thrombin (alpha)Haematologic Technologies IncorporatedHCT-0020 Human alphafor cleaving GFP tag
Amicon Ultra 15 mL 100K centrifugal filter tubeMilliporeUFC910008for concentrating protein
EDTAFisherE478500for stabilizing protein
400 mesh carbon-coated copper gridsTed Pella Inc.01754-Fgrids for negative stain
Quantifoil holey carbon grid (gold, 1.2/1.3 μm size/hole space, 300 mesh)Electron Microscopy SciencesQ3100AR1.3grids for Cryo-EM
Vitrobot Mark IIIFEIfor preparing sample grids by liquid ethane freezing
liquid nitrogenDura-CylUN1977
ethane gasAirgasUN1035
Solarus Plasma SystemGatanModel 950for cleaning grids before sample freezing
Tecnai Spirit electron microscopeFEIfor negative stain EM imaging
Talos Arctica electron microsocopeFEIfor screening and low resolution imaging of Cryo-EM grids
Titan Krios electron microscopeFEIfor high-resolution Cryo-EM imaging
Software
Gautomatch softwarehttp://www.mrc-lmb.cam.ac.uk/kzhang/Gautomatch/to pick particles from micrographs
Relion 2.1 softwarehttps://github.com/3dem/relionto construct 2D and 3D classification
CryoSPARC softwarehttps://cryosparc.com/to generate an initial structure model
Frealign softwarehttp://grigoriefflab.janelia.org/frealignto refine particles
Coot softwarehttps://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/to build a model
MolProbity softwarehttp://molprobity.biochem.duke.edu/to evaluate the geometries of the atomic model
SerialEM softwarehttp://bio3d.colorado.edu/SerialEM/for automated serial image stack acquisition
MortionCor2 softwarehttp://msg.ucsf.edu/em/software/motioncor2.htmlfor motion correction of summed movie stacks
GCTF softwarehttps://www.mrc-lmb.cam.ac.uk/kzhang/Gctf/for measuring defocus values in movie stacks
Phenix.real_space_refine softwarehttps://www.phenix-online.org/documentation/reference/real_space_refine.htmlfor real space refinement of the initial 3D model

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