Crystal structure of the Middle-East respiratory syndrome coronavirus papain-like protease in complex with ubiquitin (space group P63). Determined by X-ray diffraction at 2.15 Å resolution. Released 22 Oct 2014.
Explore 4RF1 in 3D Show helices and sheets RCSB PDB PDBe
4RF1 contains 17 α-helices and 30 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 |
|---|---|---|---|
| β-strand | 1484-1490 | 7 | 1 |
| β-strand | 1497-1502 | 6 | 1 |
| α-helix | 1507-1510 | 4 | |
| β-strand | 1514-1516 | 3 | 1 |
| β-strand | 1519-1520 | 2 | 1 |
| α-helix | 1528-1530 | 3 | |
| β-strand | 1534-1537 | 4 | 1 |
| α-helix | 1543-1553 | 11 | |
| α-helix | 1560-1570 | 11 | |
| α-helix | 1571-1573 | 3 | |
| β-strand | 1576-1579 | 4 | 2 |
| β-strand | 1582-1585 | 4 | 2 |
| α-helix | 1586-1587 | 2 | |
| α-helix | 1592-1601 | 10 | |
| β-strand | 1607-1609 | 3 | 3 |
| α-helix | 1612-1623 | 12 | |
| α-helix | 1627-1636 | 10 | |
| α-helix | 1647-1655 | 9 | |
| β-strand | 1658-1660 | 3 | 3 |
| β-strand | 1665-1672 | 8 | 4 |
| β-strand | 1676-1683 | 8 | 4 |
| α-helix | 1684-1688 | 5 | |
| β-strand | 1689-1691 | 3 | 5 |
| α-helix | 1696-1699 | 4 | |
| α-helix | 1702 | 1 | |
| β-strand | 1703-1706 | 4 | 4 |
| β-strand | 1712-1722 | 11 | 4 |
| β-strand | 1725-1737 | 13 | 5 |
| β-strand | 1746-1751 | 6 | 5 |
| β-strand | 1757 | 1 | 6 |
| β-strand | 1759-1765 | 7 | 5 |
| β-strand | 1770-1774 | 5 | 5 |
| β-strand | 1777-1781 | 5 | 5 |
| β-strand | 1783-1793 | 11 | 5 |
| β-strand | 1796-1799 | 4 | 4 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 2-6 | 5 | 7 |
| β-strand | 12-16 | 5 | 7 |
| β-strand | 22 | 1 | 8 |
| α-helix | 23-31 | 9 | |
| α-helix | 38-40 | 3 | |
| β-strand | 41-45 | 5 | 7 |
| β-strand | 48-49 | 2 | 7 |
| α-helix | 50-51 | 2 | |
| β-strand | 55 | 1 | 8 |
| α-helix | 57-59 | 3 | |
| β-strand | 66-71 | 6 | 7 |
| β-strand | 74 | 1 | 6 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| ORF1ab protein | A | protein | 324 | Human betacoronavirus 2c Jordan-N3/2012 | M4STU1 |
| Ubiquitin-60S ribosomal protein L40 | B | protein | 75 | Homo sapiens | P62987 (AlphaFold model) |
>4RF1_1 ORF1ab protein (chains A) TQQLTIEVLVTVDGVNFRTVVLNNKNTYRSQLGCVFFNGADISDTIPDEKQNGHSLYLAD NLTADETKALKELYGPVDPTFLHRFYSLKAAVHGWKMVVCDKVRSLKLSDNNCYLNAVIM TLDLLKDIKFVIPALQHAFMKHKGGDSTDFIALIMAYGNCTFGAPDDASRLLHTVLAKAE LCCSARMVWREWCNVCGIKDVVLQGLKACCYVGVQTVEDLRARMTYVCQCGGERHRQLVE HTTPWLLLSGTPNEKLVTTSTAPDFVAFNVFQGIETAVGHYVHARLKGGLILKFDSGTVS KTSDWKCKVTDVLFPGQKYSSDCN
>4RF1_2 Ubiquitin-60S ribosomal protein L40 (chains B) MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN IQKESTLHLVLRLRG
Crystal Structure of the Middle East Respiratory Syndrome Coronavirus (MERS-CoV) Papain-like Protease Bound to Ubiquitin Facilitates Targeted Disruption of Deubiquitinating Activity to Demonstrate Its Role in Innate Immune Suppression. Bailey-Elkin, B.A., Knaap, R.C., Johnson, G.G. et al. J Biol Chem (2014) 289:34667-34682. DOI 10.1074/jbc.M114.609644 · PubMed
Other PDB entries of the same protein (UniProt M4STU1), best resolution first:
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