4O4R: Murine Norovirus RdRp

Murine Norovirus RdRp in complex with PPNDS. Determined by X-ray diffraction at 2.4 Å resolution. Released 5 Nov 2014.

Method: X-ray diffraction
Resolution: 2.4 Å
Organism: Murine norovirus 1
Chains: 3
Atoms: 12,407
Mol. weight: 179.91 kDa
Ligands: 20V
Released: 5 Nov 2014

Explore 4O4R in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4O4R contains 90 α-helices and 78 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: 29 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	8-9	2	1
β-strand	12-13	2	1
β-strand	14-17	4	2
α-helix	20-24	5
β-strand	27-31	5	3
α-helix	36-38	3
β-strand	43-44	2	4
α-helix	45-46	2
α-helix	59-67	9
α-helix	68-71	4
α-helix	73-74	2
α-helix	76-79	4
α-helix	80-95	16
α-helix	98-100	3
α-helix	102-105	4
α-helix	106-112	7
β-strand	118	1	5
β-strand	126	1	5
α-helix	127-130	4
β-strand	131	1	6
β-strand	136	1	6
α-helix	138-152	15
β-strand	160-165	6	2
β-strand	169-170	2	4
α-helix	173-176	4
α-helix	182	1
β-strand	183-186	4	2
α-helix	189-207	19
β-strand	215	1	7
α-helix	221-233	13
β-strand	237-239	3	7
β-strand	243	1	8
α-helix	247-249	3
α-helix	252-264	13
α-helix	269-280	12
β-strand	283-286	4	2
β-strand	290-294	5	2
α-helix	305-325	21
α-helix	329-334	6
β-strand	336-341	6	7
β-strand	344-349	6	7
α-helix	355-364	10
β-strand	369	1	8
β-strand	382	1	7
β-strand	389-390	2	9
β-strand	393-397	5	9
β-strand	402-406	5	9
α-helix	408-416	9
β-strand	417-423	7	3
α-helix	428	1
β-strand	429	1	3
α-helix	430	1
α-helix	437-448	12
α-helix	452-467	16
α-helix	478-486	9

Chain B: 32 helices, 26 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
β-strand	8-9	2	10
β-strand	12-13	2	10
β-strand	14-17	4	11
α-helix	20-24	5
β-strand	27-31	5	12
α-helix	36-38	3
β-strand	43-44	2	13
α-helix	45-46	2
α-helix	59-67	9
α-helix	68-71	4
α-helix	73-74	2
α-helix	76-79	4
α-helix	80-95	16
α-helix	98-100	3
α-helix	102-105	4
α-helix	106-112	7
β-strand	118	1	14
β-strand	126	1	14
α-helix	127-130	4
β-strand	131	1	15
β-strand	136	1	15
α-helix	138-152	15
β-strand	160-165	6	11
β-strand	169-170	2	13
α-helix	173-176	4
β-strand	183-186	4	11
α-helix	187-188	2
α-helix	189-208	20
β-strand	215	1	16
α-helix	225-233	9
β-strand	237-239	3	16
β-strand	242-243	2	17
α-helix	247-249	3
α-helix	252-264	13
α-helix	269-280	12
α-helix	282	1
β-strand	283-286	4	11
β-strand	290-294	5	11
α-helix	305-325	21
α-helix	329-334	6
β-strand	336-341	6	16
β-strand	344-349	6	16
α-helix	355-364	10
β-strand	369-370	2	17
α-helix	378-380	3
β-strand	382	1	16
β-strand	389-390	2	18
β-strand	393-398	6	18
β-strand	401-406	6	18
α-helix	407	1
α-helix	408-416	9
β-strand	417-423	7	12
β-strand	429	1	12
α-helix	430-431	2
α-helix	438-448	11
α-helix	452-468	17
α-helix	478-486	9

Chain C: 29 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	8-9	2	19
β-strand	12-13	2	19
β-strand	14-17	4	20
α-helix	20-24	5
β-strand	27-31	5	21
β-strand	43-44	2	22
α-helix	48-50	3
α-helix	59-67	9
α-helix	68-70	3
α-helix	73-74	2
α-helix	76-79	4
α-helix	80-95	16
α-helix	98-100	3
α-helix	102-105	4
α-helix	106-112	7
β-strand	118	1	23
β-strand	126	1	23
α-helix	127-130	4
β-strand	131	1	24
β-strand	136	1	24
α-helix	138-153	16
β-strand	160-165	6	20
β-strand	169-170	2	22
α-helix	172-174	3
β-strand	183-186	4	20
α-helix	187-188	2
α-helix	189-208	20
β-strand	215	1	25
α-helix	221-233	13
β-strand	237-239	3	25
β-strand	242-243	2	26
α-helix	252-264	13
α-helix	269-280	12
β-strand	283-286	4	20
β-strand	290-294	5	20
α-helix	305-325	21
α-helix	329-334	6
β-strand	336-341	6	25
β-strand	344-349	6	25
α-helix	355-364	10
β-strand	369-370	2	26
β-strand	382	1	25
β-strand	389-390	2	27
β-strand	393-398	6	27
β-strand	401-406	6	27
α-helix	407	1
α-helix	408-416	9
β-strand	417-423	7	21
α-helix	428	1
β-strand	429	1	21
α-helix	430	1
α-helix	437-448	12
α-helix	452-467	16
α-helix	475-477	3
α-helix	478-487	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
RNA-dependent-RNA-polymerase	A, B, C	protein	515	Murine norovirus 1	Q80J95 (AlphaFold model)

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

>4O4R_1 RNA-dependent-RNA-polymerase (chains A, B, C)
MLPRPSGTYAGLPIADYGDAPPLSTKTMFWRTSPEKLPPGAWEPAYLGSKDERVDGPSLQ
QVMRDQLKPYSEPRGLLPPQEILDAVCDAIENRLENTLEPQKPWTFKKACESLDKNTSSG
YPYHKQKSKDWTGSAFIGDLGDQATHANNMYEMGKSMRPIYTAALKDELVKPDKIYGKIK
KRLLWGSDLGTMIRAARAFGPFCDALKETCIFNPIRVGMSMNEDGPFIFARHANFRYHMD
ADYTRWDSTQQRAILKRAGDIMVRLSPEPDLARVVMDDLLAPSLLDVGDYKIVVEEGLPS
GCPCTTQLNSLAHWILTLCAMVEVTRVDPDIVMQESEFSFYGDDEVVSTNLELDMVKYTM
ALRRYGLLPTRADKEEGPLERRQTLQGISFLRRAIVGDQFGWYGRLDRASIDRQLLWTKG
PNHQNPFETLPGHAQRPSQLMALLGEAAMHGEKYYRTVASRVSKEAAQSGIEMVVPRHRS
VLRWVRFGTMDAETPQERSAVFVNEDELEHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
20V	3-[(E)-{4-formyl-5-hydroxy-6-methyl-3-[(phosphonooxy)methyl]pyridin-2-yl}diazen…	C18 H15 N4 O14 P S2	6

Water and common crystallization additives (SO4) are not listed.

Primary citation

PPNDS inhibits murine Norovirus RNA-dependent RNA-polymerase mimicking two RNA stacking bases. Croci, R., Tarantino, D., Milani, M. et al. FEBS Lett (2014) 588:1720-1725. DOI 10.1016/j.febslet.2014.03.021 · 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…
4X2V 2.3 Å, Crystal structure of the Murine Norovirus NS6 protease (inactive C139A mutant) with a…
8A8X 2.37 Å, TRIM7 PRYSPRY in complex with a MNV1-NS3 peptide HDDFGLQ
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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