5W8U: 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 2.41 Å resolution. Released 27 Sept 2017.

Method: X-ray diffraction
Resolution: 2.41 Å
Organisms: Human betacoronavirus 2c EMC/2012, Homo sapiens
Chains: 4
Atoms: 6,455
Mol. weight: 90.83 kDa
Ligands: ZN, AYE
Released: 27 Sept 2017

Explore 5W8U in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5W8U contains 31 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: 12 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	1
β-strand	16-21	6	1
α-helix	26-29	4
β-strand	33-35	3	1
β-strand	38-39	2	1
α-helix	44-45	2
α-helix	47-49	3
β-strand	53-56	4	1
α-helix	62-72	11
α-helix	79-89	11
β-strand	95-98	4	2
β-strand	101-104	4	2
α-helix	111-120	10
β-strand	126-128	3	3
α-helix	131-142	12
α-helix	146-155	10
α-helix	158-159	2
α-helix	166-174	9
β-strand	177-179	3	3
β-strand	184-191	8	4
β-strand	195-202	8	4
α-helix	203-206	4
β-strand	208-210	3	5
α-helix	215-219	5
β-strand	222-225	4	4
β-strand	231-241	11	4
β-strand	244-256	13	5
β-strand	265-270	6	5
β-strand	278-285	8	5
β-strand	288-293	6	5
β-strand	296-300	5	5
β-strand	302-312	11	5
β-strand	315-318	4	4

Chain B: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	82-87	6	6
β-strand	93-98	6	6
β-strand	103	1	7
α-helix	104-115	12
α-helix	119-121	3
β-strand	122-126	5	6
β-strand	129-130	2	6
β-strand	136	1	7
α-helix	137-140	4
β-strand	147-152	6	6

Chain C: 12 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	8
β-strand	15-21	7	8
α-helix	26-29	4
β-strand	33-35	3	8
β-strand	38-39	2	8
α-helix	44-45	2
β-strand	53-56	4	8
α-helix	62-72	11
α-helix	79-89	11
β-strand	95-98	4	9
β-strand	101-104	4	9
α-helix	105-106	2
α-helix	111-120	10
β-strand	126-128	3	10
α-helix	131-141	11
α-helix	146-155	10
α-helix	158-159	2
α-helix	166-174	9
β-strand	177-179	3	10
β-strand	184-191	8	11
β-strand	195-202	8	11
α-helix	203-206	4
β-strand	208-210	3	12
α-helix	215-219	5
β-strand	222-225	4	11
β-strand	231-241	11	11
β-strand	244-256	13	12
β-strand	265-270	6	12
β-strand	278-285	8	12
β-strand	288-293	6	12
β-strand	296-300	5	12
β-strand	302-312	11	12
β-strand	315-318	4	11

Chain D: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
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
β-strand	147-152	6	13

Molecules and chains

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

Sequence of entity 1 (A, C), FASTA

>5W8U_1 ORF1ab (chains A, C)
QLTIEVLVTVDGVNFRTVVLNNKNTYRSQLGCVFFNGADISDTIPDEKQNGHSLYLADNL
TADETKALKELYGPVDPTFLHRFYSLKAAVHGWKMVVCDKVRSLKLSDNNCYLNAVIMTL
DLLKDIKFVIPALQHAFMKHKGGDSTDFIALIMAYGNCTFGAPDDASRLLHTVLAKAELC
CSARMVWREWCNVCGIKDVVLQGLKACCYVGVQTVEDLRARMTYVCQCGGERHRQLVEHT
TPWLLLSGTPNEKLVTTSTAPDFVAFNVFQGIETAVGHYVHARLKGGLILKFDSGTVSKT
SDWKCKVTDVLFPGQKYSSDCN

Sequence of entity 2 (B, D), FASTA

>5W8U_2 Ubiquitin-like protein ISG15 (chains B, D)
MEPLSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEGVQDDLFWLTFEGKPLEDQLPLG
EYGLKPLSTVFMNLRLRG

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 M4STU1), best resolution first:

4RF1 2.15 Å, Crystal structure of the Middle-East respiratory syndrome coronavirus papain-like…
5W8T 2.76 Å, Crystal structure of MERS-CoV papain-like protease in complex with the C-terminal domain…
4REZ 2.8 Å, Crystal structure of the Middle-East respiratory syndrome coronavirus papain-like protease
4RF0 2.8 Å, Crystal structure of the Middle-East respiratory syndrome coronavirus papain-like…

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