4NRU: Murine Norovirus RNA-dependent-RNA-polymerase

Murine Norovirus RNA-dependent-RNA-polymerase in complex with Compound 6, a suramin derivative. Determined by X-ray diffraction at 2.3 Å resolution. Released 15 Oct 2014.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Murine norovirus 1
Chains: 6
Atoms: 24,851
Mol. weight: 354.86 kDa
Ligands: MG, 2NG
Released: 15 Oct 2014

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

Secondary structure: helices and β-sheets

4NRU contains 167 α-helices and 146 β-strands across 6 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: 28 helices, 24 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	68-70	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	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
β-strand	183-186	4	2
α-helix	187-188	2
α-helix	189-208	20
β-strand	215	1	7
α-helix	221-232	12
β-strand	237-239	3	7
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	382	1	7
β-strand	389-390	2	8
β-strand	393-398	6	8
β-strand	401-405	5	8
α-helix	408-416	9
β-strand	417-423	7	3
β-strand	429	1	3
α-helix	430-431	2
α-helix	437-448	12
α-helix	452-463	12
α-helix	478-486	9

Chain B: 31 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	8-9	2	9
β-strand	12-13	2	9
β-strand	14-17	4	10
α-helix	20-24	5
β-strand	27-31	5	11
α-helix	36-38	3
β-strand	43-44	2	12
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	80-97	18
α-helix	99-100	2
α-helix	102-105	4
α-helix	106-112	7
β-strand	118	1	13
β-strand	126	1	13
α-helix	127-130	4
β-strand	131	1	14
β-strand	136	1	14
α-helix	138-152	15
β-strand	160-165	6	10
β-strand	169-170	2	12
α-helix	173-176	4
β-strand	183-186	4	10
α-helix	187-188	2
α-helix	189-208	20
β-strand	215	1	15
α-helix	221-233	13
β-strand	237-239	3	15
α-helix	247-249	3
α-helix	252-264	13
α-helix	269-280	12
α-helix	282	1
β-strand	283-286	4	10
β-strand	290-294	5	10
α-helix	305-325	21
α-helix	329-334	6
β-strand	336-341	6	15
β-strand	344-349	6	15
α-helix	355-364	10
α-helix	378-380	3
β-strand	382	1	15
β-strand	389-390	2	16
β-strand	393-398	6	16
β-strand	401-406	6	16
α-helix	408-416	9
β-strand	417-423	7	11
α-helix	428	1
β-strand	429	1	11
α-helix	430	1
α-helix	437-448	12
α-helix	452-467	16
α-helix	478-486	9

Chain C: 26 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	8-9	2	17
β-strand	12-13	2	17
β-strand	14-17	4	18
α-helix	20-24	5
β-strand	27-31	5	19
α-helix	36-38	3
β-strand	43-44	2	20
α-helix	59-71	13
α-helix	73-74	2
α-helix	76-79	4
α-helix	80-97	18
α-helix	98-100	3
α-helix	102-105	4
α-helix	106-112	7
β-strand	118	1	21
β-strand	126	1	21
α-helix	127-130	4
β-strand	131	1	22
β-strand	136	1	22
α-helix	138-152	15
β-strand	160-165	6	18
β-strand	169-170	2	20
α-helix	173-176	4
β-strand	183-186	4	18
α-helix	189-207	19
β-strand	215	1	23
α-helix	225-232	8
β-strand	237-239	3	23
α-helix	246-249	4
α-helix	252-264	13
α-helix	269-280	12
β-strand	283-286	4	18
β-strand	290-294	5	18
α-helix	305-325	21
α-helix	329-334	6
β-strand	336-341	6	23
β-strand	344-349	6	23
α-helix	355-364	10
β-strand	382	1	23
β-strand	389-390	2	24
β-strand	393-398	6	24
β-strand	401-405	5	24
α-helix	408-416	9
β-strand	417-423	7	19
α-helix	428	1
β-strand	429	1	19
α-helix	430	1
α-helix	437-448	12
α-helix	452-464	13
α-helix	478-486	9

Chain D: 28 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	8-9	2	25
β-strand	12-13	2	25
β-strand	14-17	4	26
α-helix	20-24	5
β-strand	27-31	5	27
α-helix	36-38	3
β-strand	43-44	2	28
α-helix	45-46	2
α-helix	59-67	9
α-helix	68-70	3
α-helix	73-74	2
α-helix	76-79	4
α-helix	80-97	18
α-helix	98-100	3
α-helix	102-105	4
α-helix	106-112	7
β-strand	118	1	29
β-strand	126	1	29
α-helix	127-130	4
β-strand	131	1	30
β-strand	136	1	30
α-helix	138-152	15
β-strand	160-165	6	26
β-strand	169-170	2	28
α-helix	173-176	4
β-strand	183-186	4	26
α-helix	187-188	2
α-helix	189-208	20
β-strand	215	1	31
α-helix	221-233	13
β-strand	237-239	3	31
β-strand	244	1	32
α-helix	247-249	3
α-helix	252-264	13
α-helix	269-280	12
β-strand	283-286	4	26
β-strand	290-294	5	26
α-helix	305-325	21
α-helix	329-334	6
β-strand	336-341	6	31
β-strand	344-349	6	31
α-helix	355-364	10
β-strand	368	1	32
α-helix	378-380	3
β-strand	382	1	31
β-strand	389-390	2	33
β-strand	393-398	6	33
β-strand	401-406	6	33
α-helix	408-416	9
β-strand	417-423	7	27
β-strand	429	1	27
α-helix	437-448	12
α-helix	452-467	16
α-helix	478-486	9

Chain E: 27 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	8	1	34
β-strand	13	1	34
β-strand	14-17	4	35
α-helix	20-24	5
β-strand	27-31	5	36
α-helix	36-38	3
β-strand	43-44	2	37
α-helix	59-67	9
α-helix	68-71	4
α-helix	73-74	2
α-helix	76-79	4
α-helix	80-97	18
α-helix	98-100	3
α-helix	102-105	4
α-helix	106-112	7
β-strand	118	1	38
β-strand	126	1	38
α-helix	127-130	4
β-strand	131	1	39
β-strand	136	1	39
α-helix	138-153	16
β-strand	160-165	6	35
β-strand	169-170	2	37
α-helix	172-174	3
β-strand	183-186	4	35
α-helix	189-207	19
β-strand	215	1	40
α-helix	221-233	13
β-strand	237-239	3	40
α-helix	247-249	3
α-helix	252-264	13
α-helix	269-280	12
β-strand	283-286	4	35
β-strand	290-294	5	35
α-helix	305-325	21
α-helix	329-334	6
β-strand	336-341	6	40
β-strand	344-349	6	40
α-helix	355-365	11
α-helix	378-381	4
β-strand	382	1	40
β-strand	389-390	2	41
β-strand	393-398	6	41
β-strand	401-406	6	41
α-helix	408-416	9
β-strand	417-423	7	36
β-strand	429	1	36
α-helix	437-448	12
α-helix	452-463	12
α-helix	475-477	3
α-helix	478-486	9

Chain F: 27 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	8-9	2	42
β-strand	12-13	2	42
β-strand	14-17	4	43
α-helix	20-24	5
β-strand	27-31	5	44
α-helix	36-38	3
β-strand	43-44	2	45
α-helix	59-71	13
α-helix	73-74	2
α-helix	76-79	4
α-helix	80-97	18
α-helix	98-100	3
α-helix	102-105	4
α-helix	106-111	6
β-strand	118	1	46
β-strand	126	1	46
α-helix	127-130	4
β-strand	131	1	47
β-strand	136	1	47
α-helix	138-153	16
β-strand	160-165	6	43
β-strand	169-170	2	45
α-helix	173-176	4
β-strand	183-186	4	43
α-helix	187-188	2
α-helix	189-208	20
β-strand	215	1	48
α-helix	221-233	13
β-strand	237-239	3	48
α-helix	252-264	13
α-helix	269-280	12
β-strand	283-286	4	43
β-strand	290-294	5	43
α-helix	305-325	21
α-helix	329-334	6
β-strand	336-341	6	48
β-strand	344-349	6	48
α-helix	355-365	11
α-helix	378-380	3
β-strand	382	1	48
β-strand	389-390	2	49
β-strand	393-398	6	49
β-strand	401-406	6	49
α-helix	408-416	9
β-strand	417-423	7	44
α-helix	428	1
β-strand	429	1	44
α-helix	430-431	2
α-helix	438-448	11
α-helix	451-462	12
α-helix	478-486	9

Molecules and chains

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

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

>4NRU_1 RNA dependent RNA polymerase (chains A, B, C, D, E, F)
MLPRPSGTYAGLPIADYGDAPPLSTKTMFWRTSPEKLPPGAWEPAYLGSKDERVDGPSLQ
QVMRDQLKPYSEPRGLLPPQEILDAVCDAIENRLENTLEPQKPWTFKKACESLDKNTSSG
YPYHKQKSKDWTGSAFIGDLGDQATHANNMYEMGKSMRPIYTAALKDELVKPDKIYGKIK
KRLLWGSDLGTMIRAARAFGPFCDALKETCIFNPIRVGMSMNEDGPFIFARHANFRYHMD
ADYTRWDSTQQRAILKRAGDIMVRLSPEPDLARVVMDDLLAPSLLDVGDYKIVVEEGLPS
GCPCTTQLNSLAHWILTLCAMVEVTRVDPDIVMQESEFSFYGDDEVVSTNLELDMVKYTM
ALRRYGLLPTRADKEEGPLERRQTLQGISFLRRAIVGDQFGWYGRLDRASIDRQLLWTKG
PNHQNPFETLPGHAQRPSQLMALLGEAAMHGEKYYRTVASRVSKEAAQSGIEMVVPRHRS
VLRWVRFGTMDAETPQERSAVFVNEDELEHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	6
2NG	4-({4-methyl-3-[(3-nitrobenzoyl)amino]benzoyl}amino)naphthalene-1,5-disulfonic…	C25 H19 N3 O10 S2	7

Primary citation

Structural bases of norovirus RNA dependent RNA polymerase inhibition by novel suramin-related compounds. Croci, R., Pezzullo, M., Tarantino, D. et al. PLoS One (2014) 9:e91765-e91765. DOI 10.1371/journal.pone.0091765 · 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…
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
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…

Browse structure collections

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