Extended Data Table 3.
a. Inter-subunit contact surface area Å2. | ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Subunit | Apc1 | Apc2 | Apc3 | Apc4 | Apc5 | Apc6 | Apc7 | Apc8 | Apc10 | Apc11 | Apc12 | Apc13 | Apc15 | Apc16 | Cdh1 | Emi1 |
Apc1 | - | |||||||||||||||
Apc2 | 2520 | - | ||||||||||||||
Apc3 | 360 | 0 | 5746 | |||||||||||||
Apc4 | 0 | 714 | 0 | - | ||||||||||||
Apc5 | 8744 | 0 | 0 | 6226 | - | |||||||||||
Apc6 | 1056 | 0 | 4590 | 0 | 0 | 5244 | ||||||||||
Apc7 | 0 | 0 | 5354 | 0 | 0 | 0 | 5026 | |||||||||
Apc8 | 4290 | 0 | 0 | 0 | 3722 | 3772 | 0 | 4558 | ||||||||
Apc10 | 2616 | 0 | 2510 | 0 | 0 | 0 | 0 | 0 | - | |||||||
Apc11 | 0 | 3402 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | - | ||||||
Apc11RING | 0 | 666 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | ||||||
Apc12 | 246 | 0 | 0 | 0 | 0 | 5970 | 0 | 0 | 0 | 0 | - | |||||
Apc13 | 0 | 0 | 836 | 0 | 0 | 2068 | 0 | 3240 | 0 | 0 | 0 | - | ||||
Apc15 | 0 | 0 | 0 | 224 | 3446 | 340 | 0 | 1082 | 0 | 0 | 0 | 0 | - | |||
Apc16 | 40 | 0 | 2514 | 0 | 0 | 222 | 1502 | 0 | 0 | 0 | 0 | 0 | 0 | - | ||
Cdh1 | 1960 | 0 | 1906 | 0 | 0 | 712 | 0 | 3022 | 0 | 0 | 0 | 0 | 0 | 0 | - | |
Cdh1NTD | 1960 | 0 | 0 | 0 | 0 | 500 | 0 | 3022 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
Cdh1WD40 | 0 | 0 | 82 | 0 | 0 | 212 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
Cdh1IR | 0 | 0 | 1824 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
Emi1 | 732 | 762 | 0 | 0 | 0 | 0 | 0 | 0 | 704 | 1300 | 0 | 0 | 0 | 0 | 754 | - |
Total | 24524 | 8064 | 25722 | 7164 | 34010 | 24686 | 11882 | 26708 | 5830 | 4702 | 6216 | 6144 | 5092 | 4278 | 8354 | 4252 |
b. DALI Results | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Subunit/domain | Protein match | RCSB PDB | Z | RMSD Å | Aligned N | Res N | ID % | Subunit/domain | Protein match | RCSB PDB | Z | RMSD Å | Aligned N | Res N | ID % |
Apc1WD40 | Sc Cdh1 | 4BH6-E | 15.9 | 4.0 | 259 | 303 | 8 | Apc6 | Sp Apc6 | 2XPI-D | 36.9 | 2.2 | 481 | 520 | 37 |
Apc1PC | Sc Rpn2 | 4ADY-B | 27.8 | 3.2 | 406 | 802 | 15 | Apc7 | Sp Apc6 | 2XPI-D | 24.9 | 7.8 | 464 | 518 | 15 |
Apc2NTD | Hs Cul3 | 4HXI-B | 13.8 | 7.4 | 301 | 346 | 7 | Apc8 | Sp Apc6 | 2XPI-D | 25.5 | 7.2 | 443 | 518 | 19 |
Apc2CTD | Hs Cullin1 | 4F52-A | 23.5 | 2.2 | 237 | 258 | 18 | Apc3A | Apc3B | - | 1.6 | 482 | 497 | 100 | |
Apc5TPR | Sp Apc6 | 2XPI-A | Apc6A | Apc6B | - | 4.0 | 486 | 503 | 100 | ||||||
Apc3 | Sp Apc6 | 2XPI-A | 29.6 | 4.9 | 456 | 518 | 19 | Apc7A | Apc7B | - | 2.6 | 483 | 483 | 100 | |
Apc8A | Apc8B | - | 3.7 | 389 | 490 | 100 |
c. Surface Plasma Resonance Data | ||||||
---|---|---|---|---|---|---|
Ligand | Analyte | koff (s−1) | kon (M−1 s−1) | Keqd (nM) | Kkin d (nM) | Reference |
UbcH10 | Ternary | 0.42 ± 0.02 | 1.78 ± 0.2 × 106 | 215 | 236 ± 29 | 4 |
UbcH10LR | Ternary (fast) | 4.0 ± 0.2 × 10−2 | 1.70 ± 0.1 × 106 | 31 | 24 ± 2 | This study |
(slow) | 4.6 ± 0.2 × 10−3 | 1.70 ± 0.1 × 105 | 23 ± 5 |
Kkind is the ratio of the observed microscopic rate constants.
Calculated using CCP4. (b) Pair-wise structural comparison (DALI) of APC/C subunits. (c) Surface Plasma Resonance data. Table comparing APC/CCdh1.Hsl1 (ternary APC/C), dissociation constants for UbcH10 (Ref. 4), and UbcH10LR (this work). Keqd: Equilibrium dissociation constant; Kkind: kinetic dissociation constant = koff/kon. Standard errors of the fit are listed.