Table 2.
Rotation (translation) differences in the selected domains between the fitted structuresa)
| Protein domains | RDF b) |
MDfit
|
NMFF
|
|||
|---|---|---|---|---|---|---|
| MDfit | NMFF | YUP.SCX | NMFF | YUP.SCX | YUP.SCX | |
| EF2 | ||||||
| IV | 17.7 (3.2) | 37.1 (5.0) | 30.2 (7.3) | 23.4 (1.9) | 17.1 (4.5) | 25.5 (3.5) |
| V | 18.6 (3.1) | 38.5 (5.0) | 28.5 (7.3) | 27.1 (2.5) | 16.0 (5.7) | 15.2 (3.6) |
| EFG | ||||||
| II | 18.7 (2.0) | 23.8 (2.9) | 20.9 (2.5) | 5.6 (1.1) | 2.5 (0.6) | 4.7 (0.8) |
| V | 97.3 (2.2) | 87.8 (6.2) | 79.1 (2.3) | 21.5 (5.2) | 19.2 (1.7) | 15.8 (4.1) |
| RF3 | ||||||
| II | 20.9 (2.1) | 18.2 (2.2) | 16.0 (1.6) | 2.6 (1.4) | 6.7 (1.7) | 4.9 (1.0) |
| III | 16.2 (2.2) | 11.3 (1.3) | 4.3 (1.9) | 9.6 (1.2) | 12.5 (0.7) | 9.4 (0.8) |
| EF2′ | ||||||
| III | 17.3 (1.9) | 46.5 (5.3) | 16.3 (2.2) | 31.9 (4.2) | 1.8 (0.9) | 31.7 (3.4) |
| V | 7.3 (1.6) | 30.9 (6.8) | 17.8 (2.4) | 29.4 (5.4) | 13.7 (1.1) | 17.7 (4.7) |
Rotations (translations) differences in domains orientations between two fitted structures in degrees (Å) calculated after removing the overall transitional/rotational degrees of freedom by root mean square fitting the two structures. These are the rotations and translations needed for the domains to fit them individually to accommodate the conformational changes of domain orientations between the two structures. Rotation (translation) values > 20° (> 4 Å) are in bold and values > 15° (> 3 Å) are underlined. A complete rotation/translation table containing all domains in the proteins is provided in the Supporting Information (Table S5).
Structures reported in the PDB by rigid body fitting of individual domains of the initial structures into the corresponding cryo-EM maps.