5V69: MERS-CoV PLpro

Crystal structure of the Middle East respiratory syndrome coronavirus papain-like protease bound to ubiquitin variant ME.4. Determined by X-ray diffraction at 2.55 Å resolution. Released 10 May 2017.

Method: X-ray diffraction
Resolution: 2.55 Å
Organisms: Human betacoronavirus 2c EMC/2012, Homo sapiens
Chains: 2
Atoms: 3,152
Mol. weight: 48.61 kDa
Ligands: ZN, PGO
Released: 10 May 2017

Explore 5V69 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5V69 contains 17 α-helices and 28 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.

Chain A: 13 helices, 21 β-strands

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	1525-1526	2
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	1612-1622	11
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
β-strand	1703-1706	4	4
β-strand	1712-1721	10	4
β-strand	1724-1737	14	5
β-strand	1746-1751	6	5
β-strand	1759-1766	8	5
β-strand	1769-1773	5	5
β-strand	1778-1781	4	5
β-strand	1783-1794	12	5
β-strand	1797-1799	3	4

Chain B: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	6
β-strand	12-16	5	6
β-strand	22	1	7
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	6
β-strand	48-49	2	6
α-helix	50-51	2
β-strand	55	1	7
β-strand	66-71	6	6
α-helix	72	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
MERS-CoV PLpro	A	protein	324	Human betacoronavirus 2c EMC/2012	K0BWD0 (AlphaFold model)
ME.4	B	protein	104	Homo sapiens

Sequence of entity 1 (A), FASTA

>5V69_1 MERS-CoV PLpro (chains A)
TQQLTIEVLVTVDGVNFRTVVLNNKNTYRSQLGCVFFNGADISDTIPDEKQNGHSLYLAD
NLTADETKALKELYGPVDPTFLHRFYSLKAAVHGWKMVVCDKVRSLKLSDNNCYLNAVIM
TLDLLKDIKFVIPALQHAFMKHKGGDSTDFIALIMAYGNCTFGAPDDASRLLHTVLAKAE
LCCSARMVWREWCNVCGIKDVVLQGLKACCYVGVQTVEDLRARMTYVCQCGGERHRQLVE
HTTPWLLLSGTPNEKLVTTSTAPDFVAFNVFQGIETAVGHYVHARLKGGLILKFDSGTVS
KTSDWKCKVTDVLFPGQKYSSDCN

Sequence of entity 2 (B), FASTA

>5V69_2 ME.4 (chains B)
MAHHHHHHVTSLYKKAGSTDYKDDDDKMRIFVETLRRLTITLEVEPSDTIENVKAKIQDK
EGIPPDQQRLIFFGQQLEDGRTLSDYNIVKYSTLHLILRLNSWY

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1
PGO	S-1,2-propanediol	C3 H8 O2	2

Water and common crystallization additives (CL, NA) are not listed.

Primary citation

Potent and selective inhibition of pathogenic viruses by engineered ubiquitin variants. Zhang, W., Bailey-Elkin, B.A., Knaap, R.C.M. et al. PLoS Pathog (2017) 13:e1006372-e1006372. DOI 10.1371/journal.ppat.1006372 · PubMed

Other PDB entries of the same protein (UniProt K0BWD0 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5YNM 1.68 Å, Crystal structure of MERS-CoV nsp16/nsp10 complex bound to SAM and m7GpppA
5YNF 1.79 Å, Crystal structure of MERS-CoV nsp16/nsp10 complex bound to m7GpppA
5YNN 1.86 Å, Crystal structure of MERS-CoV nsp16/nsp10complex bound to sinefungin and m7GpppG
5YN6 1.95 Å, Crystal structure of MERS-CoV nsp10/nsp16 complex bound to SAM
5YNQ 1.96 Å, Crystal structure of MERS-CoV nsp16/nsp10 complex bound to SAH and m7GpppG
5YN5 1.96 Å, Crystal structure of MERS-CoV nsp10/nsp16 complex
5YNO 1.96 Å, Crystal structure of MERS-CoV nsp16/nsp10 complex bound to SAH and m7GpppA
5YN8 1.97 Å, Crystal structure of MERS-CoV nsp16/nsp10 complex bound to SAH
5YNB 1.98 Å, Crystal structure of MERS-CoV nsp16/nsp10 complex bound to Sinefungin
5YNJ 2.04 Å, Crystal structure of MERS-CoV nsp16/nsp10 complex bound to m7GpppG
5YNI 2.07 Å, Crystal structure of MERS-CoV nsp16/nsp10 complex bound to SAM and m7GpppG
5YNP 2.27 Å, Crystal structure of MERS-CoV nsp16/nsp10 complex bound to sinefungin and m7GpppA

Browse structure collections

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