Crystal structure of MERS-CoV nsp16/nsp10 complex bound to SAM and m7GpppA. Determined by X-ray diffraction at 1.68 Å resolution. Released 5 Dec 2018.
Explore 5YNM in 3D Show helices and sheets RCSB PDB PDBe
5YNM contains 23 α-helices and 21 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
| Element | Residues | Length | Sheet |
|---|---|---|---|
| α-helix | 2-5 | 4 | |
| β-strand | 8-10 | 3 | 1 |
| α-helix | 13-16 | 4 | |
| α-helix | 42-54 | 13 | |
| β-strand | 66-70 | 5 | 1 |
| α-helix | 80-88 | 9 | |
| β-strand | 94-99 | 6 | 1 |
| β-strand | 109-112 | 4 | 1 |
| α-helix | 115-117 | 3 | |
| β-strand | 118-120 | 3 | 2 |
| β-strand | 124-129 | 6 | 1 |
| α-helix | 134-137 | 4 | |
| α-helix | 150-159 | 10 | |
| β-strand | 161-162 | 2 | 1 |
| β-strand | 163 | 1 | 3 |
| β-strand | 164-171 | 8 | 1 |
| α-helix | 178-183 | 6 | |
| α-helix | 184-186 | 3 | |
| β-strand | 187-195 | 9 | 1 |
| α-helix | 196-198 | 3 | |
| β-strand | 204-211 | 8 | 1 |
| α-helix | 221-234 | 14 | |
| α-helix | 242-244 | 3 | |
| α-helix | 252-253 | 2 | |
| β-strand | 259-260 | 2 | 3 |
| α-helix | 264-266 | 3 | |
| α-helix | 269-276 | 8 | |
| β-strand | 281-282 | 2 | 3 |
| β-strand | 290-292 | 3 | 2 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| α-helix | 12-16 | 5 | |
| α-helix | 23-32 | 10 | |
| α-helix | 35-38 | 4 | |
| β-strand | 43 | 1 | 4 |
| α-helix | 44-45 | 2 | |
| β-strand | 55-56 | 2 | 4 |
| β-strand | 65-69 | 5 | 4 |
| α-helix | 71-73 | 3 | |
| α-helix | 75-78 | 4 | |
| β-strand | 96-100 | 5 | 4 |
| α-helix | 101-103 | 3 | |
| α-helix | 107-113 | 7 | |
| β-strand | 116 | 1 | 5 |
| β-strand | 123 | 1 | 5 |
| β-strand | 126-127 | 2 | 5 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| nsp16 protein | A | protein | 303 | Human betacoronavirus 2c EMC/2012 | K0BWD0 (AlphaFold model) |
| nsp10 protein | B | protein | 140 | Human betacoronavirus 2c EMC/2012 | K4LC41 (AlphaFold model) |
>5YNM_1 nsp16 protein (chains A) ASADWKPGHAMPSLFKVQNVNLERCELANYKQSIPMPRGVHMNIAKYMQLCQYLNTCTLA VPANMRVIHFGAGSDKGIAPGTSVLRQWLPTDAIIIDNDLNEFVSDADITLFGDCVTVRV GQQVDLVISDMYDPTTKNVTGSNESKALFFTYLCNLINNNLALGGSVAIKITEHSWSVEL YELMGKFAWWTVFCTNANASSSEGFLLGINYLGTIKENIDGGAMHANYIFWRNSTPMNLS TYSLFDLSKFQLKLKGTPVLQLKESQINELVISLLSQGKLLIRDNDTLSVSTDVLVNTYR KLR
>5YNM_2 nsp10 protein (chains B) AGSNTEFASNSSVLSLVNFTVDPQKAYLDFVNAGGAPLTNCVKMLTPKTGTGIAISVKPE STADQETYGGASVCLYCRAHIEHPDVSGVCKYKGKFVQIPAQCVRDPVGFCLSNTPCNVC QYWIGYGCNCDSLRQAALPQ
| ID | Name | Formula | Copies |
|---|---|---|---|
| ZN | Zinc ion | Zn | 2 |
| GTA | P1-7-methylguanosine-P3-adenosine-5',5'-triphosphate | C21 H30 N10 O17 P3 | 1 |
| SAM | S-adenosylmethionine | C15 H22 N6 O5 S | 1 |
Structural insights into the molecular mechanism of MERS Coronavirus RNA ribose 2'-O-methylation by nsp16/nsp10 protein complex. Wei, S.M., Yang, L., Ke, Z.H. et al. To be published.
Other PDB entries of the same protein (UniProt K0BWD0 (AlphaFold model), which also has an AlphaFold model), best resolution first:
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