TABLE 6.
The volumes of six cavities in the cytoplasmic side of BR structures 1F50 (Br state), 1F4Z (early M state), and 1JV7 (O-like state)
| BR (1F50) | M (1F4Z) | O (1JV7) | |||||
|---|---|---|---|---|---|---|---|
| Color* | Volume | Boundary helices | Volume | Boundary helices | Volume | Boundary helices | |
| Blue† | 1 | 71 | A, B, C, G | 93 | A, B, C, G | 95 | A, B, C, G |
| Green‡ | 3 | 18 | C, E, F | 66 | C, E, F | 53 | C, E, F |
| Orange§ | 4 | 23 | B, C, F, G | 27 | C, F, G | 34 | B, C, F, G |
| Purple¶ | 6 | Too small | – | 14 | A, B, G | – | – |
| Yellow‖ | 7 | 21 | C, D, E | Fractured | – | 19 | C, D, E |
| Lilac** | 8 | 9.7 | C, D | 7.5 | D, E | Fractured | – |
Bold numbers correspond with cavities that expanded significantly during the Br → Early M transition. The volume is given in Å3 units.
Color of the corresponding cavities in Fig. 2
Contributing atoms: 1F50: Helix A: F27:CE2; Helix B: I45:CG2; T46:CA, O, CG2; V49:CB, CG1, CG2; P50:CD; Helix C: L93:CA, CD2; D96:OD2; Helix G:K216:CA, C, O; F219:CD1; G220:CA. 1F4Z: Helix A:F27:CE2; Helix B: I45:CG2; T46:CA, O, OG1, CG2; V49:CB, CG1, CG2; P50:CD; Helix C: L93:CD1; D96:OD2; Helix G:A215:O; K216:CA, C, O; F219:CB, CD1;G220:N, C; L223:CB, CD2. 1JV7: Helix A: F27:CE1; Helix B: I45:CG2; T46:CA, O, CG2; V49:CB, CG1, CG2; P50:CB, CG, CD; Helix C: L92:C, O, CA, CD2, CB, OD1; Helix G: K216:CA, C, O, CB; V217:CA, CD2, CE2; G220:CA; L223:CD2.
Contributing atoms: 1F50: Helix C: L97:CD1; Helix E: L152:CB, CD1, CD2; Helix F: F171:CE1; R175:CA, CB, CG. 1F4Z: Helix C: L97:CD1, CD2; Helix E: L149:CA, O, CD2; L152:CB, CD1, CD2 F153:N, CA, CB; Helix F: F171:CE1, CZ, CA; R175:O, CB, CG; T178:CB, CG2; V179:CG2. 1JV7: Helix C: L97:CG, CD1, CD2; Helix E: L152:CB, CD1, CD2; F171:CD1, CE1, CZ; L174:C, CB; Helix F: R175:N, CA, O, CB, CG; T178:CB, CG2; V179:CG2.
Contributing atoms: 1F50: Helix B: F42:CD1, CE1; Helix C:D96:C, O, CB; L97:CD2;L100:CD1, CD2; Helix F: L174:CD1; Helix G: F219:CZ; L223:CD1, CD2. 1F4Z: Helix C: D96:C, O, CB; L97: CD2; L100:CD2; Helix F: L174:CD1; Helix G: F219:CE1, CZ, CD1; L223:CD2. 1JV7: Helix B: F42:CD2, CE2; Helix C: D96:C, O, CB; L97:CA, CD1; L100:CG, CD1; Helix F: L174:CD1; Helix G: F219:CE2, CZ; L223:CD1, CD2.
Contributing atoms: 1F4Z: Helix A: F27: CB; Helix B: Y43:CA, O, CD1; T46:C, CB, OG1; Helix G: L224:CD1. In 1F50 and 1JV7, this cavity becomes too small to be detected with a probe radius of 1 Å.
Contributing atoms: 1F50: Helix C: L94:CA, O, CB, CD2; L97:CB; A98:N, CA, CB; Helix D: L111: CD1; Helix E: L152:CD2; F156:CE2, CZ. 1JV7: Helix C: L94:CA, O, CB, CD2; L97:CB; A98:CB; Helix D: L111:CD1; Helix E: L152:CD2; F156:CE2. In 1F4Z, this cavity is accessible to the bulk, and hence is not detected by our screening.
Contributing atoms: 1F50: Helix C: A98:CB; Loop: A103:CB; Helix D: T107:C, CG2; I108:N, CA, CG1; L111:CD1. 1F4Z: Loop: A103:CB; Helix D: T107:C, CG2; I108:N, CA, CG1; L111: CD1; Helix E: F156:CZ. In 1JV7, this cavity is accessible to the bulk, and hence is not detected by our screening.