7UV5: Papain-like protease nsp3

The crystal structure of Papain-Like Protease of SARS CoV-2, C111S/D286N mutant, in complex with a Lys48-linked di-ubiquitin. Determined by X-ray diffraction at 1.45 Å resolution. Released 11 May 2022.

Method: X-ray diffraction
Resolution: 1.45 Å
Organisms: Severe acute respiratory syndrome coronavirus 2, Homo sapiens
Chains: 3
Atoms: 3,869
Mol. weight: 53.42 kDa
Ligands: ZN
Released: 11 May 2022

Explore 7UV5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7UV5 contains 18 α-helices and 33 β-strands across 3 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, 22 β-strands

Element	Residues	Length	Sheet
β-strand	5-10	6	1
β-strand	17-21	5	1
α-helix	27-31	5
β-strand	34-36	3	1
β-strand	39-40	2	1
α-helix	44-46	3
α-helix	48-50	3
β-strand	54-57	4	1
α-helix	62-72	11
α-helix	79-90	12
β-strand	97-98	2	2
β-strand	101-102	2	2
α-helix	111-120	10
β-strand	127	1	3
α-helix	130-140	11
α-helix	145-155	11
β-strand	163	1	4
α-helix	165-173	9
β-strand	176	1	3
β-strand	182-189	8	5
β-strand	193-200	8	5
α-helix	201-204	4
β-strand	206-208	3	4
α-helix	213-218	6
β-strand	220-223	4	5
β-strand	229-238	10	5
β-strand	241-253	13	4
α-helix	254	1
β-strand	260-266	7	4
β-strand	271-278	8	4
β-strand	282-286	5	4
β-strand	289-293	5	4
β-strand	296-306	11	4
β-strand	309-311	3	5

Chain B: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	6
α-helix	11	1
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	1
β-strand	55	1	7
β-strand	66-71	6	6
β-strand	75	1	4

Chain C: 2 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	24-28	5
α-helix	38-40	3
β-strand	41-45	5	8
β-strand	48-49	2	8
β-strand	68-71	4	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Papain-like protease nsp3	A	protein	318	Severe acute respiratory syndrome coronavirus 2	P0DTD1 (AlphaFold model)
Ubiquitin	B	protein	76	Homo sapiens	P0CG48 (AlphaFold model)
Ubiquitin	C	protein	76	Homo sapiens	P0CG47 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7UV5_1 Papain-like protease nsp3 (chains A)
SNAEVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYV
LPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQVNGLTSIKWADNNSYLATAL
LTLQQIELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHAN
LDSCKRVLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQ
ESPFVMMSAPPAQYELKHGTFTCASEYTGNYQCGHYKHITSKETLYCINGALLTKSSEYK
GPITDVFYKENSYTTTIK

Sequence of entity 2 (B), FASTA

>7UV5_2 Ubiquitin (chains B)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Sequence of entity 3 (C), FASTA

>7UV5_3 Ubiquitin (chains C)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGRQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1

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

Primary citation

Dual domain recognition determines SARS-CoV-2 PLpro selectivity for human ISG15 and K48-linked di-ubiquitin. Wydorski, P.M., Osipiuk, J., Lanham, B.T. et al. Nat Commun (2023) 14:2366-2366. DOI 10.1038/s41467-023-38031-5 · PubMed

Other PDB entries of the same protein (UniProt P0DTD1 (AlphaFold model), which also has an AlphaFold model), best resolution first:

44PS 0.77 Å, 6-conformation model of SARS-CoV-2 NSP3 macrodomain (C2 crystal form, 100 K)
7KR0 0.77 Å, Crystal structure of SARS-CoV-2 NSP3 macrodomain (C2 crystal form, 100 K)
9CY0 0.8 Å, Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with AVI-4206
7TX0 0.84 Å, Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ADP-ribose at pH 9 (P43…
7KQO 0.85 Å, Crystal structure of SARS-CoV-2 NSP3 macrodomain (P43 crystal form)
7HCO 0.87 Å, PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in…
7KQP 0.88 Å, Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ADP-ribose (P43 crystal…
7TWJ 0.9 Å, Crystal structure of SARS-CoV-2 NSP3 macrodomain at pH 4 (P43 crystal form)
7TWN 0.9 Å, Crystal structure of SARS-CoV-2 NSP3 macrodomain at pH 5 (P43 crystal form)
7TWO 0.9 Å, Crystal structure of SARS-CoV-2 NSP3 macrodomain at pH 6 (P43 crystal form)
7TWP 0.9 Å, Crystal structure of SARS-CoV-2 NSP3 macrodomain at pH 7 (P43 crystal form)
7TWQ 0.9 Å, Crystal structure of SARS-CoV-2 NSP3 macrodomain at pH 9 (P43 crystal form)

Browse structure collections

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