4X2V: NS6 Protease

Crystal structure of the Murine Norovirus NS6 protease (inactive C139A mutant) with a C-terminal extension to include residue P1 prime of NS7. Determined by X-ray diffraction at 2.3 Å resolution. Released 18 Feb 2015.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Murine norovirus 1
Chains: 6
Atoms: 5,356
Mol. weight: 78.75 kDa
Released: 18 Feb 2015

Explore 4X2V in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4X2V contains 12 α-helices and 60 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: 4 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	2-4	3
α-helix	6-8	3
β-strand	9-12	4	1
β-strand	15-19	5	1
β-strand	24-28	5	1
α-helix	29-31	3
α-helix	33-34	2
β-strand	39	1	2
β-strand	42	1	2
β-strand	47-52	6	1
β-strand	55-60	6	1
β-strand	72-73	2	3
β-strand	82-88	7	3
β-strand	93-105	13	3
β-strand	109	1	4
β-strand	112	1	4
β-strand	116-121	6	3
β-strand	142-147	6	3
β-strand	150-160	11	3
β-strand	166-170	5	3

Chain B: 4 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	6-8	3
β-strand	9-12	4	5
β-strand	15-19	5	5
β-strand	24-28	5	5
α-helix	29-31	3
β-strand	39	1	6
β-strand	42	1	6
β-strand	47-52	6	5
β-strand	55-60	6	5
α-helix	69-70	2
β-strand	72-73	2	3
β-strand	82-88	7	3
α-helix	89	1
β-strand	94-109	16	3
β-strand	112-121	10	3
β-strand	142-147	6	3
β-strand	150-160	11	3
β-strand	166-170	5	3

Chain C: 2 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	6-8	3
β-strand	9-12	4	7
β-strand	15-19	5	7
β-strand	24-28	5	7
α-helix	29-31	3
β-strand	39	1	8
β-strand	42	1	8
β-strand	47-52	6	7
β-strand	55-60	6	7
β-strand	72-73	2	9
β-strand	82-88	7	9
β-strand	93-108	16	9
β-strand	113-121	9	9
β-strand	142-147	6	9
β-strand	150-160	11	9
β-strand	166-170	5	9

Chain D: 2 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	6-8	3
β-strand	9-12	4	10
β-strand	15-19	5	10
β-strand	24-28	5	10
α-helix	29-31	3
β-strand	39	1	11
β-strand	42	1	11
β-strand	47-52	6	10
β-strand	55-60	6	10
β-strand	72-73	2	9
β-strand	82-88	7	9
β-strand	94-106	13	9
β-strand	115-121	7	9
β-strand	127	1	12
β-strand	130	1	12
β-strand	142-147	6	9
β-strand	150-160	11	9
β-strand	166-170	5	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
NS6 Protease	A, B, C, D	protein	185	Murine norovirus 1	Q80J95 (AlphaFold model)
NS6 Protease	E	protein	5	Murine norovirus 1	Q80J95 (AlphaFold model)
NS6 Protease	F	protein	7	Murine norovirus 1

Sequence of entity 1 (A, B, C, D), FASTA

>4X2V_1 NS6 Protease (chains A, B, C, D)
SAPVSIWSRVVQFGTGWGFWVSGHVFITAKHVAPPKGTEIFGRKPGDFTVTSSGDFLKYY
FTSAVRPDIPAMVLENGCQEGVVASVLVKRASGEMLALAVRMGSQAAIKIGSAVVHGQTG
MLLTGSNAKAQDLGTIPGDAGCPYVYKKGNTWVVIGVHVAATRSGNTVIAATHGEPTLEA
LEFQG

Sequence of entity 2 (E), FASTA

>4X2V_2 NS6 Protease (chains E)
LEFQG

Sequence of entity 3 (F), FASTA

>4X2V_3 NS6 Protease (chains F)
XXXXXXX

Primary citation

Structure determination of Murine Norovirus NS6 proteases with C-terminal extensions designed to probe protease-substrate interactions. Fernandes, H., Leen, E.N., Cromwell, H. et al. PeerJ (2015) 3:e798-e798. DOI 10.7717/peerj.798 · PubMed

Other PDB entries of the same protein (UniProt Q80J95 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4ASH 1.58 Å, Crystal structure of the NS6 protease from murine norovirus 1
3UQS 2.0 Å, Crystal structures of murine norovirus RNA-dependent RNA polymerase
3SFG 2.21 Å, crystal structure of murine norovirus RNA dependent RNA polymerase in complex with…
4NRU 2.3 Å, Murine Norovirus RNA-dependent-RNA-polymerase in complex with Compound 6, a suramin…
8A8X 2.37 Å, TRIM7 PRYSPRY in complex with a MNV1-NS3 peptide HDDFGLQ
4O4R 2.4 Å, Murine Norovirus RdRp in complex with PPNDS
4X2Y 2.42 Å, Crystal structure of a chimeric Murine Norovirus NS6 protease (inactive C139A mutant) in…
3UR0 2.45 Å, Crystal structures of murine norovirus RNA-dependent RNA polymerase in complex with…
4X2X 2.47 Å, Crystal structure of the Murine Norovirus NS6 protease (inactive C139A mutant) with a…
3QID 2.5 Å, Crystal structures and functional analysis of murine norovirus RNA-dependent RNA…
3SFU 2.5 Å, crystal structure of murine norovirus RNA dependent RNA polymerase in complex with…
3NAI 2.56 Å, Crystal structures and functional analysis of murine norovirus RNA-dependent RNA…

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