6YVA: PLpro-C111S with mISG15

PLpro-C111S with mISG15. Determined by X-ray diffraction at 3.18 Å resolution. Released 13 May 2020.

Method: X-ray diffraction
Resolution: 3.18 Å
Organisms: Severe acute respiratory syndrome coronavirus 2, Mus musculus
Chains: 2
Atoms: 3,407
Mol. weight: 53.64 kDa
Ligands: ZN
Released: 13 May 2020

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

Secondary structure: helices and β-sheets

6YVA contains 16 α-helices and 35 β-strands across 2 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: 9 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	5-10	6	1
β-strand	17-21	5	1
β-strand	35-36	2	1
β-strand	39-40	2	1
α-helix	45-47	3
β-strand	54-56	3	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	145-154	10
β-strand	163	1	4
α-helix	165-174	10
β-strand	176	1	3
β-strand	182-183	2	5
β-strand	199-200	2	5
α-helix	202-204	3
β-strand	208	1	6
β-strand	237-238	2	5
β-strand	241-253	13	6
α-helix	254	1
β-strand	260-266	7	6
β-strand	271-277	7	6
β-strand	283-286	4	6
β-strand	289-291	3	6
β-strand	296-306	11	6

Chain C: 7 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	7
β-strand	14-20	7	7
β-strand	24	1	8
α-helix	25-36	12
α-helix	40-42	3
β-strand	43-46	4	7
β-strand	51	1	7
α-helix	52-53	2
β-strand	57	1	8
β-strand	68-73	6	7
β-strand	80-85	6	9
β-strand	91-96	6	9
β-strand	101	1	10
α-helix	102-113	12
α-helix	117-119	3
β-strand	121-124	4	9
β-strand	127-128	2	9
α-helix	129-130	2
β-strand	134	1	10
α-helix	136-138	3
β-strand	145-149	5	9
β-strand	154	1	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Replicase polyprotein 1a	A	protein	315	Severe acute respiratory syndrome coronavirus 2	P0DTD1 (AlphaFold model)
Ubiquitin-like protein ISG15	C	protein	161	Mus musculus	Q64339 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6YVA_1 Replicase polyprotein 1a (chains A)
EVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPN
DDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQVNGLTSIKWADNNSYLATALLTL
QQIELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDS
CKRVLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESP
FVMMSAPPAQYELKHGTFTCASEYTGNYQCGHYKHITSKETLYCIDGALLTKSSEYKGPI
TDVFYKENSYTTTIK

Sequence of entity 2 (C), FASTA

>6YVA_2 Ubiquitin-like protein ISG15 (chains C)
MAWDLKVKMLGGNDFLVSVTNSMTVSELKKQIAQKIGVPAFQQRLAHQTAVLQDGLTLSS
LGLGPSSTVMLVVQNCSEPLSILVRNERGHSNIYEVFLTQTVDTLKKKVSQREQVHEDQF
WLSFEGRPMEDKELLGEYGLKPQCTVIKHLRLRGGGGDQCA

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1

Primary citation

Papain-like protease regulates SARS-CoV-2 viral spread and innate immunity. Shin, D., Mukherjee, R., Grewe, D. et al. Nature (2020) 587:657-662. DOI 10.1038/s41586-020-2601-5 · 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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