Crystal structure of MERS-CoV nsp16/nsp10complex bound to sinefungin and m7GpppG. Determined by X-ray diffraction at 1.86 Å resolution. Released 5 Dec 2018.
Explore 5YNN in 3D Show helices and sheets RCSB PDB PDBe
5YNN contains 24 α-helices and 23 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 | 34-36 | 3 | |
| α-helix | 37-39 | 3 | |
| α-helix | 42-54 | 13 | |
| β-strand | 66-70 | 5 | 1 |
| β-strand | 78 | 1 | 2 |
| α-helix | 80-88 | 9 | |
| β-strand | 94-99 | 6 | 1 |
| β-strand | 104 | 1 | 2 |
| β-strand | 109-112 | 4 | 1 |
| α-helix | 115-117 | 3 | |
| β-strand | 118-120 | 3 | 3 |
| 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 | 4 |
| β-strand | 164-171 | 8 | 1 |
| α-helix | 178-183 | 6 | |
| α-helix | 184-186 | 3 | |
| β-strand | 187-195 | 9 | 1 |
| 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 | 4 |
| α-helix | 264-266 | 3 | |
| α-helix | 269-276 | 8 | |
| β-strand | 281-282 | 2 | 4 |
| β-strand | 290-292 | 3 | 3 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| α-helix | 11-16 | 6 | |
| α-helix | 23-32 | 10 | |
| α-helix | 35-38 | 4 | |
| β-strand | 43 | 1 | 5 |
| α-helix | 44-45 | 2 | |
| β-strand | 55-56 | 2 | 5 |
| β-strand | 65-69 | 5 | 5 |
| α-helix | 71-73 | 3 | |
| α-helix | 75-78 | 4 | |
| β-strand | 96-100 | 5 | 5 |
| α-helix | 101-103 | 3 | |
| α-helix | 107-112 | 6 | |
| β-strand | 116 | 1 | 6 |
| β-strand | 123 | 1 | 6 |
| β-strand | 126-127 | 2 | 6 |
| 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) |
>5YNN_1 nsp16 protein (chains A) ASADWKPGHAMPSLFKVQNVNLERCELANYKQSIPMPRGVHMNIAKYMQLCQYLNTCTLA VPANMRVIHFGAGSDKGIAPGTSVLRQWLPTDAIIIDNDLNEFVSDADITLFGDCVTVRV GQQVDLVISDMYDPTTKNVTGSNESKALFFTYLCNLINNNLALGGSVAIKITEHSWSVEL YELMGKFAWWTVFCTNANASSSEGFLLGINYLGTIKENIDGGAMHANYIFWRNSTPMNLS TYSLFDLSKFQLKLKGTPVLQLKESQINELVISLLSQGKLLIRDNDTLSVSTDVLVNTYR KLR
>5YNN_2 nsp10 protein (chains B) AGSNTEFASNSSVLSLVNFTVDPQKAYLDFVNAGGAPLTNCVKMLTPKTGTGIAISVKPE STADQETYGGASVCLYCRAHIEHPDVSGVCKYKGKFVQIPAQCVRDPVGFCLSNTPCNVC QYWIGYGCNCDSLRQAALPQ
| ID | Name | Formula | Copies |
|---|---|---|---|
| ZN | Zinc ion | Zn | 2 |
| GTG | 7-methyl-guanosine-5'-triphosphate-5'-guanosine | C21 H30 N10 O18 P3 | 1 |
| SFG | Sinefungin | C15 H23 N7 O5 | 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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