In situ atomic-resolution structure of the baseplate antenna complex in Chlorobaculum tepidum obtained combining solid-state NMR spectroscopy, cryo electron microscopy and polarization spectroscopy
ELECTRON MICROSCOPY - SOLID-STATE NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D 13C-13C DARR | 10.0 % [U-13C; U-15N] CsmA, 10.0 % [U-13C; U-15N] BACTERIOCHLOROPHYLL A, 35.0 % [U-13C] Carotenoids, 35.0 % [U-13C] Lipids, 10.0 % n.a. Magnesium ion | solid state, lyophylized | 0.0 M | 7.0 | 1 atm | 280 | Bruker AVANCE II 700 |
| 2 | 3D NCACX | 10.0 % [U-13C; U-15N] CsmA, 10.0 % [U-13C; U-15N] BACTERIOCHLOROPHYLL A, 35.0 % [U-13C] Carotenoids, 35.0 % [U-13C] Lipids, 10.0 % n.a. Magnesium ion | solid state, lyophylized | 0.0 M | 7.0 | 1 atm | 280 | Bruker AVANCE II 700 |
| 3 | 3D NCOCX | 10.0 % [U-13C; U-15N] CsmA, 10.0 % [U-13C; U-15N] BACTERIOCHLOROPHYLL A, 35.0 % [U-13C] Carotenoids, 35.0 % [U-13C] Lipids, 10.0 % n.a. Magnesium ion | solid state, lyophylized | 0.0 M | 7.0 | 1 atm | 280 | Bruker AVANCE II 700 |
| 4 | 3D CANCO | 10.0 % [U-13C; U-15N] CsmA, 10.0 % [U-13C; U-15N] BACTERIOCHLOROPHYLL A, 35.0 % [U-13C] Carotenoids, 35.0 % [U-13C] Lipids, 10.0 % n.a. Magnesium ion | solid state, lyophylized | 0.0 M | 7.0 | 1 atm | 280 | Bruker AVANCE II 700 |
| 5 | 3D CONCA | 10.0 % [U-13C; U-15N] CsmA, 10.0 % [U-13C; U-15N] BACTERIOCHLOROPHYLL A, 35.0 % [U-13C] Carotenoids, 35.0 % [U-13C] Lipids, 10.0 % n.a. Magnesium ion | solid state, lyophylized | 0.0 M | 7.0 | 1 atm | 280 | Bruker AVANCE II 700 |
| 6 | 2D NCA | 10.0 % [U-13C; U-15N] CsmA, 10.0 % [U-13C; U-15N] BACTERIOCHLOROPHYLL A, 35.0 % [U-13C] Carotenoids, 35.0 % [U-13C] Lipids, 10.0 % n.a. Magnesium ion | solid state, lyophylized | 0.0 M | 7.0 | 1 atm | 280 | Bruker AVANCE II 700 |
| 7 | 2D NCO | 10.0 % [U-13C; U-15N] CsmA, 10.0 % [U-13C; U-15N] BACTERIOCHLOROPHYLL A, 35.0 % [U-13C] Carotenoids, 35.0 % [U-13C] Lipids, 10.0 % n.a. Magnesium ion | solid state, lyophylized | 0.0 M | 7.0 | 1 atm | 280 | Bruker AVANCE II 700 |
| 8 | 2D 13C-13C DARR | 10.0 % [U-13C; U-15N] CsmA, 10.0 % [U-13C; U-15N] BACTERIOCHLOROPHYLL A, 35.0 % [U-13C] Carotenoids, 35.0 % [U-13C] Lipids, 10.0 % n.a. Magnesium ion | solid state, lyophylized | 0.0 M | 7.0 | 1 atm | 280 | Bruker AVANCE II 500 |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | AVANCE II | 700 |
| 2 | Bruker | AVANCE II | 500 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| torsion angle dynamics | Xplor-NIH | |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | target function |
| Conformers Calculated Total Number | 80 |
| Conformers Submitted Total Number | 1 |
| Representative Model | 1 (target function and agreement with back-calculated cd spectra) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 5 | refinement | Xplor-NIH | 2.33 | Charles Schwieters, Marius Clore |
| 2 | structure calculation | GASyCS | Nielsen | |
| 4 | peak picking | Sparky | Goddard | |
| Sample |
|---|
| Carotenosome organelle consisting of csma proteins and bchla antenna molecules. |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK II |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 1790 |
| Reported Resolution (Å) | 26.5 |
| Resolution Method | FSC 0.5 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C1 |
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN ULTRASCAN 4000 (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 8 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TITAN KRIOS |
| Minimum Defocus (nm) | |
| Maximum Defocus (nm) | |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | FEI TITAN KRIOS AUTOGRID HOLDER |
| Nominal Magnification | 59000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | EMAN | 2 |
| IMAGE ACQUISITION | EPU | |
| CTF CORRECTION | CTFFIND | 3 |
| INITIAL EULER ASSIGNMENT | EMAN | 2 |
| FINAL EULER ASSIGNMENT | Strul | |
| CTF CORRECTION | SPIDER | |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING ONLY | 1790 | |||
