Table 1.
Compilation of membrane protein structures determined by single particle electron cryomicroscopy to 10 Å or below (till April 2015)
| Protein | Source | Molecular mass (in MDa) | Medium | Detector | No. of particlesa | No. of asymmetric unitsa | Resolution (Å)b | EMDB | Ref |
|---|---|---|---|---|---|---|---|---|---|
| Complex I | Native (bovine) | 1 | Cymal-7 | Falcon II | 25,492 | 25,492 | ∼5 | 2676 | [58•] |
| V/A-ATPase | Native (Thermus thermophilus) | 0.6 | DDM | Film | 46,105 | 46,105 | 9 | 5335 | [47•] |
| Native (Manduca sexta)c | 0.9 | C12E10 | Falcon II | 6714 | 6714 | 9.4 | 2781 | [61•] | |
| Native (S.cerevisiae) | 0.9 | DDM | K2 | 50,030 | 50,030 | 6.9d | 6284 | [64•] | |
| F1Fo-ATPase | Native (Polytomella sp.) | 1.6 | DDM | Falcon II | 37,238 | 74,476 | ∼7 | 2852 | [60•] |
| Glutamate receptorc | Recombinant | 0.4 | DDM | Falcon II | 21,360 | 42,720 | 7.6 | 2685 | [57•] |
| Ryanodine receptorc | Native (rabbit skeletal muscle) | 2.2 | Nanodisc | Falcon II | 25,000 | 100,000 | 6.1 | 2751 | [38•] |
| Nanodisc | TVIPS F816 | 94,354 | 377,416 | 8.5 | 2752 | [38•] | |||
| CHAPS/lipids | K2 | 46,400 | 185,600 | 4.8 | 6106 | [39•] | |||
| Tween-20 | Falcon II | 65,872 | 263,488 | 3.8 | 2807 | [37•] | |||
| DDM | CCD | 28,036 | 112,144 | 9.5 | 1275 | [45] | |||
| CHAPS | Film | 25,722 | 102,888 | 10.2 | 5014 | [46] | |||
| TRPV1 | Recombinant | 0.3 | Amphipol A8-35 | K2 | 37,310 | 149,240 | 3.3d | 5778 | [55••] |
| TRPA1 | Recombinant | 0.7 | PMAL-C8 | K2 | 20,733 | 82,932 | ∼4d | 6268 | [63•] |
| γ-Secretase | Recombinant | 0.17 | Amphipol A8-35 | K2 | 144,545 | 144,545 | 4.5 | 2677 | [56•] |
| Digitonin | K2 | 177,207 | 177,207 | 4.3 | 2974 | [65] | |||
| Tmr AB+ AH5 | Recombinant | 0.18 | DDM | K2 | 102,000 | 102,000 | 8.2 | 6085 | [59•] |
| Tmr AB | Recombinant | 0.135 | DDM | TVIPS F816 | 36,000 | 36,000 | 10 | 6087 | [59•] |
| Anthrax prepore toxin | Recombinant | 0.44 | NP-40 | K2 | 60,455 | 423,185 | 2.9 | 6224 | [62•] |
| Ribosome complexese | 2.6–4.3 | ||||||||
| Sec61 | Native (porcine) | Digitonin | Falcon II | 80,019 | 80,019 | 3.35–3.9 | 2644, 46, 49, 50 | [66] | |
| Native (Canis sp.) | Digitonin | TVIPS F416 | 162,655 | 162,655 | 6.9 | 2510 | [50] | ||
| Ssh1 | Native (yeast), Ssh1(R) | Digitonin | Film | 183,000 | 183,000 | 6.1 | 1651 | [48] | |
| SecYEG | Native (E. coli) | Nanodisc | Film | 85,664 | 85,664 | 7.1 | 1858 | [49] | |
| SecYEG (R) | |||||||||
| SecYEβ | Native (M. jannaschii) | DDM | Film | 37,000 | 37,000 | 9 | 5691 | [53] | |
| SecYEβ (R) | |||||||||
| Sec61+OST+TRAP | Native (Triticum or Canis sp.) | Digitonin | TVIPS F416 | 15,705 | 15,705 | 9.3 | 2523 | [52] | |
| Digitonin | Film | 79,000 | 79,000 | 8.7 | 1528 | [51] | |||
| YidC | Native (E. coli) YidC (R) |
DDM | TVIPS F416 | 58,960 | 58,960 | 8.0 | 2705 | [54] |
Number of particles denotes the number used in the final map and number of asymmetric units is the total number averaged after the application of symmetry.
The criteria used to estimate the resolution is the Fourier shell correlation (FSC) either at FSC at 0.143 or 0.5. The numbers denoted in bold are reported at FSC 0.5.
The structure of V-ATPase from Manduca sexta, glutamate receptor and the early structures of ryanodine receptor (taken on film or CCD) have an overall resolution of 10 Å or better. However, the membrane domain is of lower resolutions and TM helices are not clearly resolved.
Multiple maps of V-type ATPase, TrpV1 and TrpA1 have been deposited and only the highest resolution is shown in the table. Three conformational states of V-ATPase have been resolved and they are deposited in EMDB codes 6284–86. The structures of TrpV1 with ligands are deposited in EMDB codes 5776–77 and please refer to Cao et al. 2013 for details of the structures [95•]. Similarly, the structures of TrpA1 with other ligands are deposited in EMDB codes 6267 and 6269.
A collection of membrane proteins in complex with ribosomes are listed here. There are many more maps deposited in the database describing different states and the list here is only a small collection chosen based on the species and describing only the highest resolution map. The resolution shown is the overall resolution and in many of these maps, the membrane protein is of lower resolution, sometimes the TM-helices in the membrane domain is not clearly resolved. The translocon proteins SSh1, SecYEG (E. coli) and SecYE (M. jannaschii) and YidC are all recombinant (shown in brackets as ‘R’), while the ribosomes used in the study are native.
Abbreviations used in the table: EMDB: electron microscopy data base; DDM: n-dodecyl-β-maltopyranoside; Cymal-7: 7-cyclohexyl-1-heptyl-β-maltoside; PMAL-C8: poly(maleic anhydride-alt-1-decene) substituted with 3-(dimethylamino) propylamine; C12E10: polyoxyethylene(10) dodecylether; NP-40: Nonidet P-40; OST: oligosaccharyl-transferase; TRPV1: transient receptor potential V1; TRPA1: known for its extensive ankyrin repeats at the amino terminal domain; TRAP: translocon associated protein complex.