7RBS: Papain-Like Protease of SARS CoV-2, C111S mutant

The crystal structure of Papain-Like Protease of SARS CoV-2, C111S mutant, in complex with human ISG15. Determined by X-ray diffraction at 2.98 Å resolution. Released 29 Sept 2021.

Method: X-ray diffraction
Resolution: 2.98 Å
Organisms: Severe acute respiratory syndrome coronavirus 2, Homo sapiens
Chains: 10
Atoms: 18,482
Mol. weight: 266.49 kDa
Ligands: ZN
Released: 29 Sept 2021

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

Secondary structure: helices and β-sheets

7RBS contains 98 α-helices and 177 β-strands across 10 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	4-10	7	1
β-strand	17-22	6	1
α-helix	28-31	4
β-strand	34-36	3	1
β-strand	39-40	2	1
α-helix	45-47	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	165-172	8
α-helix	173-175	3
β-strand	176	1	3
β-strand	182-188	7	5
β-strand	194-200	7	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
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	310-311	2	5

Chain B: 9 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	2-9	8	6
β-strand	14-20	7	6
α-helix	25-36	12
α-helix	40-42	3
β-strand	43-48	6	6
α-helix	52	1
β-strand	53	1	6
α-helix	54-55	2
β-strand	70-75	6	6
β-strand	82-87	6	7
β-strand	93-98	6	7
β-strand	103	1	8
α-helix	104-115	12
α-helix	119-121	3
β-strand	122-126	5	7
β-strand	129-130	2	7
α-helix	131-132	2
β-strand	136	1	8
α-helix	137-140	4
α-helix	142-143	2
β-strand	147-152	6	7
β-strand	156	1	4

Chain C: 12 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	9
β-strand	17-22	6	9
α-helix	28-31	4
β-strand	34-36	3	9
β-strand	39-40	2	9
α-helix	45-47	3
α-helix	48-50	3
β-strand	54-57	4	9
α-helix	62-72	11
α-helix	79-90	12
β-strand	97	1	10
β-strand	102	1	10
α-helix	111-120	10
β-strand	127	1	11
α-helix	130-140	11
α-helix	145-154	10
β-strand	163	1	12
α-helix	165-172	8
α-helix	173-175	3
β-strand	176	1	11
β-strand	182-188	7	13
β-strand	194-200	7	13
α-helix	201-204	4
β-strand	206-208	3	12
α-helix	213-218	6
β-strand	220-223	4	13
β-strand	229-238	10	13
β-strand	241-254	14	12
β-strand	260-266	7	12
β-strand	271-278	8	12
β-strand	282-286	5	12
β-strand	289-293	5	12
β-strand	295-306	12	12
β-strand	309-311	3	13

Chain D: 8 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	14
β-strand	14-19	6	14
α-helix	25-36	12
α-helix	40-42	3
β-strand	43-48	6	14
α-helix	52	1
β-strand	53	1	14
α-helix	54-55	2
β-strand	70-75	6	14
β-strand	82-87	6	15
β-strand	95-98	4	15
β-strand	103	1	16
α-helix	104-115	12
β-strand	122-126	5	15
β-strand	129-130	2	15
α-helix	131-132	2
β-strand	136	1	16
α-helix	137-140	4
β-strand	147-152	6	15
α-helix	153-154	2
β-strand	156	1	12

Chain E: 12 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	17
β-strand	17-22	6	17
α-helix	28-31	4
β-strand	34-36	3	17
β-strand	39-40	2	17
α-helix	45-47	3
α-helix	48-50	3
β-strand	54-57	4	17
α-helix	62-72	11
α-helix	79-90	12
β-strand	97	1	18
β-strand	102	1	18
α-helix	111-120	10
β-strand	127	1	19
α-helix	130-140	11
α-helix	145-155	11
β-strand	163	1	20
α-helix	165-172	8
α-helix	173-175	3
β-strand	176	1	19
β-strand	182-188	7	21
β-strand	194-200	7	21
α-helix	202-205	4
β-strand	206-208	3	20
α-helix	213-218	6
β-strand	220-223	4	21
β-strand	229-238	10	21
β-strand	241-254	14	20
β-strand	260-266	7	20
β-strand	271-278	8	20
β-strand	282-286	5	20
β-strand	289-293	5	20
β-strand	295-306	12	20
β-strand	309-311	3	21

Chain F: 5 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	2-9	8	22
β-strand	14-20	7	22
β-strand	24	1	23
α-helix	25-36	12
α-helix	40-42	3
β-strand	43-48	6	22
β-strand	53	1	22
β-strand	59	1	23
β-strand	70-75	6	22
β-strand	82-87	6	24
β-strand	93-98	6	24
β-strand	103	1	25
α-helix	104-115	12
β-strand	122-126	5	24
β-strand	129-130	2	24
α-helix	131-132	2
β-strand	136	1	25
α-helix	137-140	4
β-strand	147-152	6	24
β-strand	156	1	20

Chain G: 12 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	26
β-strand	17-22	6	26
α-helix	28-31	4
β-strand	34-36	3	26
β-strand	39-40	2	26
α-helix	44-47	4
α-helix	48-50	3
β-strand	54-57	4	26
α-helix	62-72	11
α-helix	79-90	12
β-strand	97-98	2	27
β-strand	101-102	2	27
α-helix	111-120	10
β-strand	127	1	28
α-helix	130-139	10
α-helix	145-154	10
β-strand	163	1	29
α-helix	165-172	8
α-helix	173-175	3
β-strand	176	1	28
β-strand	182-188	7	30
β-strand	194-200	7	30
α-helix	201-204	4
β-strand	206-208	3	29
α-helix	213-218	6
β-strand	220-223	4	30
β-strand	229-238	10	30
β-strand	241-254	14	29
β-strand	260-266	7	29
β-strand	271-278	8	29
β-strand	282-286	5	29
β-strand	289-293	5	29
β-strand	295-306	12	29
β-strand	309-311	3	30

Chain H: 9 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	2-9	8	31
β-strand	14-20	7	31
α-helix	25-36	12
α-helix	40-42	3
β-strand	43-48	6	31
α-helix	52	1
β-strand	53	1	31
α-helix	54-55	2
β-strand	70-75	6	31
β-strand	82-87	6	32
β-strand	95-98	4	32
β-strand	103	1	33
α-helix	104-115	12
α-helix	119-121	3
β-strand	122-126	5	32
β-strand	129-130	2	32
α-helix	131-132	2
β-strand	136	1	33
α-helix	137-140	4
β-strand	147-152	6	32
α-helix	153-154	2
β-strand	156	1	29

2 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Papain-like protease	A, C, E, G, I	protein	318	Severe acute respiratory syndrome coronavirus 2	P0DTD1 (AlphaFold model)
Ubiquitin-like protein ISG15	B, D, F, H, J	protein	159	Homo sapiens	P05161 (AlphaFold model)

Sequence of entity 1 (A, C, E, G, I), FASTA

>7RBS_1 Papain-like protease (chains A, C, E, G, I)
SNAEVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYV
LPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQVNGLTSIKWADNNSYLATAL
LTLQQIELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHAN
LDSCKRVLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQ
ESPFVMMSAPPAQYELKHGTFTCASEYTGNYQCGHYKHITSKETLYCIDGALLTKSSEYK
GPITDVFYKENSYTTTIK

Sequence of entity 2 (B, D, F, H, J), FASTA

>7RBS_2 Ubiquitin-like protein ISG15 (chains B, D, F, H, J)
SNAGWDLTVKMLAGNEFQVSLSSSMSVSELKAQITQKIGVHAFQQRLAVHPSGVALQDRV
PLASQGLGPGSTVLLVVDKCDEPLSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEGVQ
DDLFWLTFEGKPLEDQLPLGEYGLKPLSTVFMNLRLRGG

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	5

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)

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