Table 1 Tested cases for template matching
From: High-confidence 3D template matching for cryo-electron tomography
Tomograms species | Tested template | TM parameters | ||
|---|---|---|---|---|
Name (species) | Reference | Angular step (deg) | pixel size (Å) | |
D. discoideum | ||||
(Tomograms analyzed: 30) | NPC (D. discoideum) | EMD-19139 | 10 | 8.7 |
Software: STOPGAP and GAPSTOPTM | NPC subunit: C8-symmetric rotational segment (D. discoideum) | EMD-19139 | 30, 20, 10, 5 | 8.7 |
NPC subunit: C8-symmetric rotational segment (H. sapiens) | PDB-id: 7R5J | 10 | 8.7 | |
Modeled vault (D. discoideum) | Swiss model | 10 | 8.7 | |
Modeled half vault (D. discoideum) | Swiss model | 10 | 8.7 | |
STA vault (D. discoideum) | This work56 | 30, 20, 10, 5 | 8.7 | |
Ribosome 80S (D. discoideum) | EMD-15810 | 30, 20, 10, 5 | 8.7 and 4.35 | |
Small ribosomal subunit 40S (D. discoideum) | This work56 | 10 | 4.35 | |
Large ribosomal subunit 60S (D. discoideum) | This work56 | 10, 5 | 4.35 | |
Unrotated ribosome (D. discoideum) | EMD-15812 | 10 | 4.35 | |
Rotated ribosome (D. discoideum) | EMD-15815 | 10 | 4.35 | |
Microtubule (H. sapiens) | EMD-6351 | 10 | 8.7 | |
Protofilament (H. sapiens) | EMD-6351 | 10, 5 | 2.446 | |
αβ-tubulin dimer (H. sapiens) | EMD-6351 | 5 | 2.446 | |
Proteasome 20S (H. sapiens) | EMD-4877 | 10 | 4.35 | |
Membrane - small STA | This work56 | 20, 10, 2 | 8.7 | |
Membrane - large STA | This work56 | 20, 10, 2 | 8.7 | |
Membrane from MD - atomistic model | This work56 | 20, 10, 2 | 8.7 | |
S. pombe | NPC subunit: C8-symmetric rotational segment (S. pombe) | EMD-11373 | 5 | 13.48 |
(Tomograms analyzed: 1) | Ribosome 80S (S. pombe) | EMD-14426 | 5 | 13.48 |
Software: STOPGAP | Fatty acid synthase - FAS (S. pombe) | EMD-14412 | 5 | 13.48 |
Membrane - large STA | This work56 | 2 | 13.48 | |
Hek293 cells | Protofilament (H. sapiens) | EMD-6351 | 5 | 4.884 |
(Tomograms analyzed: 1) | ||||
Software: GAPSTOPTM | ||||
