5W8T: MERS-CoV papain-like protease

Crystal structure of MERS-CoV papain-like protease in complex with the C-terminal domain of human ISG15. Determined by X-ray diffraction at 2.76 Å resolution. Released 27 Sept 2017.

Method: X-ray diffraction
Resolution: 2.76 Å
Organisms: Homo sapiens, Human betacoronavirus 2c EMC/2012
Chains: 4
Atoms: 6,293
Mol. weight: 90.59 kDa
Ligands: ZN, AYE
Released: 27 Sept 2017

Explore 5W8T in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5W8T contains 35 α-helices and 56 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: 14 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	3
β-strand	15-21	7	3
α-helix	26-29	4
β-strand	33-35	3	3
β-strand	38-39	2	3
α-helix	44-45	2
α-helix	47-49	3
β-strand	53-56	4	3
α-helix	62-72	11
α-helix	79-89	11
α-helix	90-92	3
β-strand	95-98	4	4
β-strand	101-104	4	4
α-helix	105-106	2
α-helix	111-122	12
β-strand	126-128	3	5
α-helix	131-140	10
α-helix	146-155	10
α-helix	158-159	2
α-helix	166-174	9
β-strand	177-179	3	5
β-strand	184-191	8	6
β-strand	195-202	8	6
α-helix	203-207	5
β-strand	208-210	3	7
α-helix	215-219	5
β-strand	222-225	4	6
β-strand	231-241	11	6
β-strand	244-256	13	7
β-strand	265-270	6	7
β-strand	278-285	8	7
β-strand	288-292	5	7
β-strand	297-300	4	7
β-strand	302-312	11	7
β-strand	315-318	4	6

Chains B and D: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	82-87	6	1
β-strand	93-98	6	1
β-strand	103	1	2
α-helix	104-114	11
α-helix	119-121	3
β-strand	122-126	5	1
β-strand	129-130	2	1
α-helix	131-132	2
β-strand	136	1	2
α-helix	137-140	4
β-strand	147-152	6	1

Chain C: 13 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	10
β-strand	16-21	6	10
α-helix	26-29	4
β-strand	33-35	3	10
β-strand	38-39	2	10
α-helix	44-45	2
α-helix	47-49	3
β-strand	53-56	4	10
α-helix	62-72	11
α-helix	79-89	11
α-helix	90-92	3
β-strand	95-98	4	11
β-strand	101-104	4	11
α-helix	111-122	12
β-strand	126-128	3	12
α-helix	131-140	10
α-helix	146-156	11
α-helix	158-159	2
α-helix	166-174	9
β-strand	177-179	3	12
β-strand	184-191	8	13
β-strand	195-202	8	13
α-helix	203-206	4
β-strand	208-210	3	14
α-helix	215-219	5
β-strand	222-225	4	13
β-strand	231-241	11	13
β-strand	244-256	13	14
β-strand	265-270	6	14
β-strand	278-285	8	14
β-strand	288-292	5	14
β-strand	297-300	4	14
β-strand	302-312	11	14
β-strand	315-318	4	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-like protein ISG15	B, D	protein	78	Homo sapiens	P05161 (AlphaFold model)
ORF1ab	A, C	protein	322	Human betacoronavirus 2c EMC/2012	M4STU1

Sequence of entity 1 (B, D), FASTA

>5W8T_1 Ubiquitin-like protein ISG15 (chains B, D)
MEPLSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEGVQDDLFWLTFEGKPLEDQLPLG
EYGLKPLSTVFMNLRLRG

Sequence of entity 2 (A, C), FASTA

>5W8T_2 ORF1ab (chains A, C)
QLTIEVLVTVDGVNFRTVVLNNKNTYRSQLGCVFFNGADISDTIPDEKQNGHSLYLADNL
TADETKALKELYGPVDPTFLHRFYSLKAAVHGWKMVVCDKVRSLKLSDNNCYLNAVIMTL
DLLKDIKFVIPALQHAFMKHKGGDSTDFIALIMAYGNCTFGAPDDASRLLHTVLAKAELC
CSARMVWREWCNVCGIKDVVLQGLKACCYVGVQTVEDLRARMTYVCQCGGERHRQLVEHT
TPWLLLSGTPNEKLVTTSTAPDFVAFNVFQGIETAVGHYVHARLKGGLILKFDSGTVSKT
SDWKCKVTDVLFPGQKYSSDCN

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	6
AYE	prop-2-en-1-amine	C3 H7 N	2

Water and common crystallization additives (MPD) are not listed.

Primary citation

Structurally Guided Removal of DeISGylase Biochemical Activity from Papain-Like Protease Originating from Middle East Respiratory Syndrome Coronavirus. Daczkowski, C.M., Goodwin, O.Y., Dzimianski, J.V. et al. J Virol (2017) 91. DOI 10.1128/JVI.01067-17 · PubMed

Other PDB entries of the same protein (UniProt P05161 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6FFA 1.5 Å, FMDV Leader protease bound to substrate ISG15
3PHX 1.6 Å, OTU Domain of Crimean Congo Hemorrhagic Fever Virus in complex with ISG15
3RT3 2.01 Å, Complex of influenza virus protein with host anti-viral factor
7S6P 2.15 Å, The crystal structure of human ISG15
3SDL 2.29 Å, Crystal structure of human ISG15 in complex with NS1 N-terminal region from influenza B…
6BI8 2.29 Å, X-ray structure of MERS coronavirus papain-like protease in complex with human ISG15
3PSE 2.3 Å, Structure of a viral OTU domain protease bound to interferon-stimulated gene 15 (ISG15)
3R66 2.3 Å, Crystal structure of human ISG15 in complex with NS1 N-terminal region from influenza…
5W8U 2.41 Å, Crystal structure of MERS-CoV papain-like protease in complex with the C-terminal domain…
1Z2M 2.5 Å, Crystal Structure of ISG15, the Interferon-Induced Ubiquitin Cross Reactive Protein
9NN9 2.59 Å, ISG15 complexed with nanobody
5TL6 2.62 Å, Crystal structure of SARS-CoV papain-like protease in complex with the C-terminal domain…

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