Table 1.
Cryo-EM data collection, refinement and validation statistics.
| hIP3R3 apo (EMD-7978) (PDB 6DQJ) | hIP3R3 IP3 class 1 (EMB-7981) (PDB 6DQN) | hIP3R3 IP3 class 2 (EB-7984) (PDB 6DQV) | hIP3R3 IP3 class 3 (EMB-7983) (PDB 6DQS) | hIP3R3 IP3 class 4 (EMB-7986) (PDB 6DQZ) | hIP3R3 IP3 class 5 (EMB-7987) (PDB 6DR0) | hIP3R3 Ca2+-bound (EMB-7988) (PDB 6DR2) | hIP3R3 Low IP3-Ca2+ (EMB-7991) (PDB 6DRA) | hIP3R3 High IP3-Ca2+ (EMB-7994) (PDB 6DRC) | |
|---|---|---|---|---|---|---|---|---|---|
| Data collection and processing | |||||||||
| Magnification | 105,000x | 22,500x | 22,500x | 22,500x | 22,500x | 22,500x | 22,500x | 22,500x | 22,500x |
| Voltage (kV) | 300kV | 300kV | 300kV | 300kV | 300kV | 300kV | 300kV | 300kV | 300kV |
| Electron exposure (e–/Å2) | 60 | 61 | 61 | 61 | 61 | 61 | 61 | 61 | 61 |
| Defocus range (μm) | −1.0 – 2.5 | −1.0 – 2.5 | −1.0 – 2.5 | −1.0 – 2.5 | −1.0 – 2.5 | −1.0 – 2.5 | −1.0 – 2.5 | −1.0 – 2.5 | −1.0 – 2.5 |
| Pixel size (Å) | 1.096 | 1.088 | 1.088 | 1.088 | 1.088 | 1.088 | 1.088 | 1.088 | 1.088 |
| Symmetry imposed | C4 | C4 | C4 | C1 | C1 | C1 | C4 | C4 | C4 |
| Initial particle images (no.) | 52,767 | 302,966 | 302,966 | 302,966 | 302,966 | 302,966 | 49,060 | 74,277 | 170,308 |
| Final particle images (no.) | 26,325 | 38,777 | 40,531 | 37,910 | 9,535 | 27,334 | 33,807 | 49,087 | 131,437 |
| Map resolution (Å) | 3.49 | 3.33 | 3.82 | 4.12 | 6.01 | 4.47 | 4.33 | 3.96 | 3.92 |
| FSC threshold | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 |
| Map resolution range (Å) | 300-3.49 | 300-3.33 | 300-3.82 | 300-4.12 | 300-6.01 | 300-4.47 | 300-4.33 | 300-3.96 | 300-3.92 |
| Refinement | |||||||||
| Initial model used (PDB code) | 3UJ4 | ||||||||
| Model resolution (Å) | 3.80/3.35 | 3.88/3.36 | 4.53/3.93 | 4.83/3.90 | 7.63/6.33 | 7.06/4.23 | 7.44/4.34 | 4.49/3.91 | 4.43/3.92 |
| FSC threshold | 0.50/0.143 | 0.50/0.143 | 0.50/0.143 | 0.50/0.143 | 0.50/0.143 | 0.50/0.143 | 0.50/0.143 | 0.50/0.143 | 0.50/0.143 |
| Model resolution range (Å) | 300-3.5 | 300-3.3 | 300-3.8 | 300-4.1 | 300-6.0 | 300-4.5 | 300-4.3 | 300-4.0 | 300-4.0 |
| Map sharpening B factor (Å2) | −90 | −90 | −90 | −90 | −90 | −90 | −90 | −90 | −90 |
| Model composition | |||||||||
| Non-hydrogen | 69,220 | 69,412 | 70,144 | 69,600 | 69,828 | 69,986 | 69,3572 | 69,572 | 69,508 |
| Protein residues | 8,744 | 8,744 | 8,752 | 8,750 | 8,748 | 8,750 | 8,764 | 8,764 | 8,744 |
| Ligands | 4 | 8 | 8 | 8 | 8 | 8 | 12 | 12 | 16 |
| Mean B factors (Å2) | |||||||||
| Protein | 95.1 | 116.1 | 169.0 | 193.5 | 376.7 | 217.0 | 239.9 | 240.0 | 217.9 |
| Ligand | 53.5 | 96.95 | 133.0 | 177.4 | 362.0 | 182.9 | 174.7 | 163.6 | 263.3 |
| R.m.s. deviations | |||||||||
| Bond lengths (Å) | 0.007 | 0.003 | 0.005 | 0.003 | 0.003 | 0.003 | 0.004 | 0.003 | 0.004 |
| Bond angles (°) | 0.688 | 0.490 | 0.648 | 0.520 | 0.536 | 0.538 | 0.660 | 0.517 | 0.623 |
| Validation | |||||||||
| MolProbity score | 1.53 | 1.21 | 1.36 | 1.28 | 1.22 | 1.26 | 1.26 | 1.24 | 1.33 |
| Clashscore | 2.16 | 2.09 | 2.22 | 2.41 | 2.43 | 2.37 | 2.07 | 2.96 | 2.14 |
| Poor rotamers (%) | 1.97 | 1.06 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.42 | 0.00 |
| Ramachandran plot | |||||||||
| Favored (%) | 95.52 | 96.70 | 94.74 | 96.14 | 96.8 | 96.33 | 95.91 | 97.12 | 95.04 |
| Allowed (%) | 4.48 | 3.30 | 5.26 | 3.86 | 3.20 | 3.67 | 4.09 | 2.88 | 4.96 |
| Disallowed (%) | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |