6BI8: MERS coronavirus papain-like protease

X-ray structure of MERS coronavirus papain-like protease in complex with human ISG15. Determined by X-ray diffraction at 2.29 Å resolution. Released 7 Nov 2018.

Method: X-ray diffraction
Resolution: 2.29 Å
Organisms: Human betacoronavirus 2c EMC/2012, Homo sapiens
Chains: 4
Atoms: 6,893
Mol. weight: 93.57 kDa
Ligands: ZN, AYE, CIT
Released: 7 Nov 2018

Explore 6BI8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6BI8 contains 35 α-helices and 55 β-strands across 4 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: 10 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	1544-1553	10
α-helix	1560-1570	11
β-strand	1576-1579	4	1
β-strand	1582-1585	4	1
α-helix	1586-1587	2
α-helix	1592-1601	10
β-strand	1607-1609	3	2
α-helix	1612-1622	11
α-helix	1627-1636	10
α-helix	1647-1655	9
β-strand	1658-1660	3	2
β-strand	1665-1672	8	3
β-strand	1676-1683	8	3
α-helix	1684-1688	5
β-strand	1689-1691	3	4
α-helix	1696-1700	5
β-strand	1703-1706	4	3
β-strand	1712-1721	10	3
β-strand	1724-1737	14	4
α-helix	1741-1742	2
β-strand	1746-1751	6	4
β-strand	1759-1766	8	4
β-strand	1769-1774	6	4
β-strand	1777-1781	5	4
β-strand	1783-1794	12	4
β-strand	1797-1799	3	3

Chain B: 11 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	1544-1553	10
α-helix	1560-1570	11
α-helix	1571-1573	3
β-strand	1576-1579	4	5
β-strand	1582-1585	4	5
α-helix	1586-1587	2
α-helix	1592-1601	10
β-strand	1607-1609	3	6
α-helix	1612-1622	11
α-helix	1627-1636	10
α-helix	1647-1655	9
β-strand	1658-1660	3	6
β-strand	1665-1672	8	7
β-strand	1676-1683	8	7
α-helix	1684-1688	5
β-strand	1689-1691	3	8
α-helix	1696-1700	5
β-strand	1703-1706	4	7
β-strand	1712-1721	10	7
β-strand	1724-1737	14	8
α-helix	1741-1742	2
β-strand	1746-1751	6	8
β-strand	1759-1766	8	8
β-strand	1769-1774	6	8
β-strand	1777-1781	5	8
β-strand	1783-1794	12	8
β-strand	1797-1799	3	7

Chain C: 6 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	7-8	2	9
β-strand	14-15	2	9
α-helix	25-36	12
α-helix	40-42	3
β-strand	43-47	5	9
β-strand	71-75	5	9
β-strand	82-87	6	10
β-strand	93-98	6	10
β-strand	103	1	11
α-helix	104-115	12
α-helix	119-121	3
β-strand	122-126	5	10
β-strand	129-130	2	10
α-helix	131-132	2
β-strand	136	1	11
α-helix	137-140	4
β-strand	147-152	6	10

Chain D: 8 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	5-9	5	12
β-strand	15-17	3	12
α-helix	25-35	11
α-helix	40-42	3
β-strand	43-47	5	12
β-strand	52-53	2	12
α-helix	54-55	2
β-strand	70-75	6	12
β-strand	82-87	6	13
β-strand	93-98	6	13
β-strand	103	1	14
α-helix	104-115	12
α-helix	119-121	3
β-strand	122-126	5	13
β-strand	129-130	2	13
α-helix	131-132	2
β-strand	136	1	14
α-helix	137-140	4
α-helix	146	1
β-strand	147-152	6	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
ORF1a	A, B	protein	259	Human betacoronavirus 2c EMC/2012	K0BWD0 (AlphaFold model)
Ubiquitin-like protein ISG15	C, D	protein	156	Homo sapiens	P05161 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6BI8_1 ORF1a (chains A, B)
NDETKALKELYGPVDPTFLHRFYSLKAAVHGWKMVVCDKVRSLKLSDNNCYLNAVIMTLD
LLKDIKFVIPALQHAFMKHKGGDSTDFIALIMAYGNCTFGAPDDASRLLHTVLAKAELCC
SARMVWREWCNVCGIKDVVLQGLKACCYVGVQTVEDLRARMTYVCQCGGERHRQLVEHTT
PWLLLSGTPNEKLVTTSTAPDFVAFNVFQGIETAVGHYVHARLKGGLILKFDSGTVSKTS
DWKCKVTDVLFPGQKYSSD

Sequence of entity 2 (C, D), FASTA

>6BI8_2 Ubiquitin-like protein ISG15 (chains C, D)
MGWDLTVKMLAGNEFQVSLSSSMSVSELKAQITQKIGVHAFQQRLAVHPSGVALQDRVPL
ASQGLGPGSTVLLVVDKSDEPLSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEGVQDD
LFWLTFEGKPLEDQLPLGEYGLKPLSTVFMNLRLRG

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2
AYE	prop-2-en-1-amine	C3 H7 N	2
CIT	Citric acid	C6 H8 O7	1

Water and common crystallization additives (PGE, GOL, EDO) are not listed.

Primary citation

Decoupling deISGylating and deubiquitinating activities of the MERS virus papain-like protease. Clasman, J.R., Everett, R.K., Srinivasan, K. et al. Antiviral Res (2020) 174:104661-104661. DOI 10.1016/j.antiviral.2019.104661 · 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

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