6ZSL: SARS-CoV-2 helicase

Crystal structure of the SARS-CoV-2 helicase at 1.94 Angstrom resolution. Determined by X-ray diffraction at 1.94 Å resolution. Released 29 Jul 2020.

Method: X-ray diffraction
Resolution: 1.94 Å
Organism: Severe acute respiratory syndrome coronavirus 2
Chains: 2
Atoms: 9,407
Mol. weight: 135.07 kDa
Ligands: ZN, PO4
Released: 29 Jul 2020

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

Secondary structure: helices and β-sheets

6ZSL contains 59 α-helices and 80 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: 31 helices, 39 β-strands

Element	Residues	Length	Sheet
β-strand	3-4	2	13
β-strand	11-12	2	13
β-strand	15-16	2	14
β-strand	24	1	14
α-helix	27-34	8
β-strand	42-43	2	14
β-strand	47	1	14
α-helix	60-62	3
β-strand	63-66	4	15
β-strand	69-72	4	15
β-strand	81-82	2	15
β-strand	84-85	2	16
β-strand	88-89	2	16
α-helix	104-111	8
β-strand	116	1	17
α-helix	117-125	9
α-helix	128-145	18
α-helix	146-148	3
α-helix	150-151	2
β-strand	152-157	6	18
β-strand	162-167	6	18
α-helix	172-175	4
β-strand	182-184	3	18
β-strand	197-201	5	18
β-strand	208-213	6	18
β-strand	224-227	4	18
α-helix	230-234	5
α-helix	241-243	3
β-strand	245	1	19
α-helix	260-265	6
α-helix	266-273	8
β-strand	275	1	19
β-strand	277-281	5	20
α-helix	288-298	11
β-strand	304-308	5	20
α-helix	311-324	14
α-helix	327-329	3
β-strand	330-333	4	20
β-strand	347-348	2	20
β-strand	355-359	5	20
α-helix	360-362	3
β-strand	366-373	8	20
α-helix	376-378	3
α-helix	381-390	10
β-strand	391-400	10	20
β-strand	414	1	17
α-helix	419-421	3
α-helix	424-431	8
β-strand	436-437	2	20
β-strand	440-441	2	21
α-helix	446-456	11
β-strand	462-463	2	21
α-helix	466-467	2
β-strand	471-475	5	22
β-strand	480-483	4	23
β-strand	486-489	4	23
α-helix	490-502	13
α-helix	504-508	5
α-helix	509	1
β-strand	510-513	4	22
α-helix	516-526	11
β-strand	530-532	3	22
α-helix	533-536	4
β-strand	541-547	7	22
α-helix	553-556	4
α-helix	558-565	8
β-strand	568-576	9	22
α-helix	579-584	6
β-strand	588-589	2	22
α-helix	590	1

Chain B: 28 helices, 41 β-strands

Element	Residues	Length	Sheet
β-strand	3-4	2	1
β-strand	11-12	2	1
β-strand	15-16	2	2
β-strand	24	1	2
α-helix	27-36	10
β-strand	42-43	2	2
β-strand	47	1	2
α-helix	60-62	3
β-strand	63-66	4	3
β-strand	69-72	4	3
β-strand	81-82	2	3
β-strand	84-85	2	4
β-strand	88-89	2	4
α-helix	104-111	8
β-strand	116	1	5
α-helix	117-125	9
α-helix	128-147	20
α-helix	150-151	2
β-strand	152-156	5	6
β-strand	162-163	2	7
β-strand	164-167	4	6
β-strand	182-187	6	6
β-strand	192-198	7	6
β-strand	200-202	3	7
β-strand	209-211	3	7
β-strand	224-226	3	6
α-helix	231-235	5
α-helix	241-243	3
β-strand	245	1	8
α-helix	263-265	3
α-helix	266-273	8
β-strand	275	1	8
β-strand	277-281	5	9
α-helix	288-298	11
β-strand	304-308	5	9
α-helix	311-324	14
α-helix	327-329	3
β-strand	330-332	3	9
β-strand	347-348	2	9
β-strand	355-359	5	9
α-helix	360-362	3
β-strand	366-373	8	9
α-helix	376-378	3
α-helix	381-390	10
β-strand	391-400	10	9
α-helix	405-408	4
β-strand	414	1	5
α-helix	419-421	3
α-helix	424-431	8
β-strand	436-437	2	9
β-strand	440-441	2	10
α-helix	446-456	11
β-strand	462-463	2	10
β-strand	471-475	5	11
β-strand	481-482	2	12
β-strand	487-488	2	12
α-helix	490-502	13
α-helix	504-508	5
α-helix	509	1
β-strand	510-513	4	11
α-helix	516-526	11
β-strand	530-532	3	11
α-helix	533-536	4
β-strand	541-547	7	11
α-helix	553-556	4
α-helix	558-565	8
β-strand	568-576	9	11
α-helix	579-584	6
β-strand	588-589	2	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
SARS-CoV-2 helicase NSP13	A, B	protein	603	Severe acute respiratory syndrome coronavirus 2	P0DTD1 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6ZSL_1 SARS-CoV-2 helicase NSP13 (chains A, B)
SMAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVT
DVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAG
DYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNR
NYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAP
TLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALY
YPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFC
TVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLE
PEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKG
VITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQG
SEYDYVIFTQTTETAHSCNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVA
TLQ

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	6
PO4	Phosphate ion	O4 P	4

Primary citation

Structure, mechanism and crystallographic fragment screening of the SARS-CoV-2 NSP13 helicase. Newman, J.A., Douangamath, A., Yadzani, S. et al. Nat Commun (2021) 12:4848-4848. DOI 10.1038/s41467-021-25166-6 · 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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6ZSL is part of these collections:

SARS-CoV-2 and COVID-19

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