5Y3D: RNA-dependent RNA polymerase

Structural insight into the interaction between RNA polymerase and VPg for norovirus replication. Determined by X-ray diffraction at 3.14 Å resolution. Released 18 Jul 2018.

Method: X-ray diffraction
Resolution: 3.14 Å
Organisms: Murine norovirus 1, Murine norovirus
Chains: 8
Atoms: 23,161
Mol. weight: 357.11 kDa
Released: 18 Jul 2018

Explore 5Y3D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5Y3D contains 172 α-helices and 156 β-strands across 8 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, 26 β-strands

Element	Residues	Length	Sheet
β-strand	11-12	2	1
β-strand	15-16	2	1
β-strand	17-20	4	2
α-helix	23-27	5
β-strand	30-34	5	3
α-helix	39-41	3
β-strand	46-47	2	4
α-helix	48-49	2
α-helix	62-70	9
α-helix	71-74	4
α-helix	76-77	2
α-helix	79-82	4
α-helix	83-100	18
α-helix	101-103	3
α-helix	105-108	4
α-helix	109-114	6
β-strand	121	1	5
β-strand	129	1	5
α-helix	130-133	4
β-strand	134	1	6
β-strand	139	1	6
α-helix	141-155	15
β-strand	163-168	6	2
β-strand	172-173	2	4
α-helix	176-179	4
β-strand	186-189	4	2
α-helix	192-211	20
β-strand	218	1	7
α-helix	224-236	13
β-strand	240-242	3	7
β-strand	246	1	8
α-helix	255-267	13
α-helix	272-283	12
β-strand	286-289	4	2
β-strand	293-297	5	2
α-helix	308-328	21
α-helix	332-337	6
β-strand	339-344	6	7
β-strand	347-352	6	7
α-helix	358-367	10
β-strand	372	1	8
α-helix	381-383	3
β-strand	385	1	7
β-strand	392-393	2	9
β-strand	396-401	6	9
β-strand	404-409	6	9
α-helix	411-419	9
β-strand	420-426	7	3
α-helix	431	1
β-strand	432	1	3
α-helix	433	1
α-helix	440-451	12
α-helix	455-469	15
α-helix	481-490	10

Chain B: 29 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	11-12	2	10
β-strand	15-16	2	10
β-strand	17-20	4	11
α-helix	23-27	5
β-strand	30-34	5	12
α-helix	39-41	3
β-strand	46-47	2	13
α-helix	48-49	2
α-helix	62-70	9
α-helix	71-74	4
α-helix	76-77	2
α-helix	79-82	4
α-helix	83-100	18
α-helix	101-103	3
α-helix	105-108	4
α-helix	109-114	6
β-strand	121	1	14
β-strand	129	1	14
α-helix	130-133	4
β-strand	134	1	15
β-strand	139	1	15
α-helix	141-155	15
β-strand	163-168	6	11
β-strand	172-173	2	13
α-helix	176-179	4
β-strand	186-189	4	11
α-helix	192-211	20
β-strand	218	1	16
α-helix	228-236	9
β-strand	240-242	3	16
β-strand	246	1	17
α-helix	255-267	13
α-helix	272-283	12
α-helix	285	1
β-strand	286-289	4	11
β-strand	293-297	5	11
α-helix	308-328	21
α-helix	332-337	6
β-strand	339-344	6	16
β-strand	347-352	6	16
α-helix	358-367	10
β-strand	372	1	17
α-helix	381-383	3
β-strand	385	1	16
β-strand	392-393	2	18
β-strand	396-401	6	18
β-strand	404-409	6	18
α-helix	411-419	9
β-strand	420-426	7	12
α-helix	431	1
β-strand	432	1	12
α-helix	433	1
α-helix	442-451	10
α-helix	455-469	15
α-helix	481-490	10

Chain C: 28 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	11-12	2	19
β-strand	15-16	2	19
β-strand	17-20	4	20
α-helix	23-27	5
β-strand	30-34	5	21
α-helix	39-41	3
β-strand	46-47	2	22
α-helix	48-49	2
α-helix	62-70	9
α-helix	71-74	4
α-helix	76-77	2
α-helix	79-82	4
α-helix	83-100	18
α-helix	101-103	3
α-helix	105-108	4
α-helix	109-114	6
β-strand	121	1	23
β-strand	129	1	23
α-helix	130-133	4
β-strand	134	1	24
β-strand	139	1	24
α-helix	141-155	15
β-strand	163-168	6	20
β-strand	172-173	2	22
α-helix	176-179	4
β-strand	186-189	4	20
α-helix	192-211	20
β-strand	218	1	25
α-helix	224-235	12
β-strand	240-242	3	25
β-strand	246	1	26
α-helix	255-267	13
α-helix	272-283	12
β-strand	286-289	4	20
β-strand	293-297	5	20
α-helix	308-328	21
α-helix	332-337	6
β-strand	339-344	6	25
β-strand	347-352	6	25
α-helix	358-367	10
β-strand	372	1	26
α-helix	381-383	3
β-strand	385	1	25
β-strand	392-393	2	27
β-strand	396-401	6	27
β-strand	404-409	6	27
α-helix	411-419	9
β-strand	420-426	7	21
α-helix	431	1
β-strand	432	1	21
α-helix	433	1
α-helix	440-451	12
α-helix	455-469	15
α-helix	481-489	9

Chain D: 27 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	11-12	2	28
β-strand	15-16	2	28
β-strand	17-20	4	29
α-helix	23-27	5
β-strand	30-34	5	30
α-helix	39-41	3
β-strand	46-47	2	31
α-helix	48-49	2
α-helix	62-70	9
α-helix	71-74	4
α-helix	76-77	2
α-helix	79-82	4
α-helix	83-100	18
α-helix	102-103	2
α-helix	105-108	4
α-helix	109-114	6
β-strand	121	1	32
β-strand	129	1	32
α-helix	130-133	4
β-strand	134	1	33
β-strand	139	1	33
α-helix	141-155	15
β-strand	163-168	6	29
β-strand	172-173	2	31
α-helix	176-179	4
β-strand	186-189	4	29
α-helix	192-211	20
β-strand	218	1	34
α-helix	228-236	9
β-strand	240-242	3	34
β-strand	246	1	35
α-helix	255-267	13
α-helix	272-283	12
α-helix	285	1
β-strand	286-289	4	29
β-strand	293-297	5	29
α-helix	308-328	21
α-helix	332-337	6
β-strand	339-344	6	34
β-strand	347-352	6	34
α-helix	358-367	10
β-strand	372	1	35
α-helix	381-383	3
β-strand	385	1	34
β-strand	392-393	2	36
β-strand	396-401	6	36
β-strand	404-408	5	36
α-helix	411-419	9
β-strand	420-426	7	30
β-strand	432	1	30
α-helix	440-451	12
α-helix	455-467	13
α-helix	481-490	10

Chain E: 28 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	11-12	2	37
β-strand	15-16	2	37
β-strand	17-20	4	38
α-helix	23-27	5
β-strand	30-34	5	39
α-helix	39-41	3
β-strand	46-47	2	40
α-helix	48-49	2
α-helix	62-70	9
α-helix	71-74	4
α-helix	76-77	2
α-helix	79-82	4
α-helix	83-100	18
α-helix	101-103	3
α-helix	105-108	4
α-helix	109-114	6
β-strand	121	1	41
β-strand	129	1	41
α-helix	130-133	4
β-strand	134	1	42
β-strand	139	1	42
α-helix	141-155	15
β-strand	163-168	6	38
β-strand	172-173	2	40
α-helix	176-179	4
β-strand	186-189	4	38
α-helix	192-211	20
β-strand	218	1	43
α-helix	224-236	13
β-strand	240-242	3	43
β-strand	246	1	44
α-helix	255-267	13
α-helix	272-283	12
β-strand	286-289	4	38
β-strand	293-297	5	38
α-helix	308-328	21
α-helix	332-337	6
β-strand	339-344	6	43
β-strand	347-352	6	43
α-helix	358-367	10
β-strand	372	1	44
α-helix	382-383	2
β-strand	385	1	43
β-strand	392-393	2	45
β-strand	396-401	6	45
β-strand	404-409	6	45
α-helix	411-419	9
β-strand	420-426	7	39
α-helix	431	1
β-strand	432	1	39
α-helix	433	1
α-helix	442-451	10
α-helix	455-470	16
α-helix	481-489	9

Chain F: 28 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	11-12	2	46
β-strand	15-16	2	46
β-strand	17-20	4	47
α-helix	23-27	5
β-strand	30-34	5	48
α-helix	39-41	3
β-strand	46-47	2	49
α-helix	48-49	2
α-helix	62-70	9
α-helix	71-74	4
α-helix	76-77	2
α-helix	79-82	4
α-helix	83-100	18
α-helix	101-103	3
α-helix	105-108	4
α-helix	109-114	6
β-strand	121	1	50
β-strand	129	1	50
α-helix	130-133	4
β-strand	134	1	51
β-strand	139	1	51
α-helix	141-155	15
β-strand	163-168	6	47
β-strand	172-173	2	49
α-helix	176-179	4
β-strand	186-189	4	47
α-helix	192-211	20
β-strand	218	1	52
α-helix	228-236	9
β-strand	240-242	3	52
β-strand	246	1	53
α-helix	255-267	13
α-helix	272-283	12
α-helix	285	1
β-strand	286-289	4	47
β-strand	293-297	5	47
α-helix	308-328	21
α-helix	332-337	6
β-strand	339-344	6	52
β-strand	347-352	6	52
α-helix	358-367	10
β-strand	372	1	53
α-helix	382-383	2
β-strand	385	1	52
β-strand	392-393	2	54
β-strand	396-401	6	54
β-strand	404-408	5	54
α-helix	411-419	9
β-strand	420-426	7	48
β-strand	432	1	48
α-helix	440-451	12
α-helix	455-469	15
α-helix	478-480	3
α-helix	481-490	10

Chain G: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	26-36	11
α-helix	42-55	14

Chain H: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	26-35	10
α-helix	42-55	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
RNA-dependent RNA polymerase	A, B, C, D, E, F	protein	517	Murine norovirus 1	Q80J95 (AlphaFold model)
viral protein genome-linked (VPg)	G, H	protein	35	Murine norovirus

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

>5Y3D_1 RNA-dependent RNA polymerase (chains A, B, C, D, E, F)
MLPRPSGTYAGLPIADYGDAPPLSTKTMFWRTSPEKLPPGAWEPAYLGSKDERVDGPSLQ
QVMRDQLKPYSEPRGLLPPQEILDAVCDAIENRLENTLEPQKPWTFKKACESLDKNTSSG
YPYHKQKSKDWTGSAFIGDLGDQATHANNMYEMGKSMRPIYTAALKDELVKPDKIYGKIK
KRLLWGSDLGTMIRAARAFGPFCDALKETCIFNPIRVGMSMNEDGPFIFARHANFRYHMD
ADYTRWDSTQQRAILKRAGDIMVRLSPEPDLARVVMDDLLAPSLLDVGDYKIVVEEGLPS
GCPCTTQLNSLAHWILTLCAMVEVTRVDPDIVMQESEFSFYGDDEVVSTNLELDMVKYTM
ALRRYGLLPTRADKEEGPLERRQTLQGISFLRRAIVGDQFGWYGRLDRASIDRQLLWTKG
PNHQNPFETLPGHAQRPSQLMALLGEAAMHGEKYYRTVASRVSKEAAQSGIEMVVPRHRS
VLRWVRFGTMDAETPQERSAVFVNEDAAALEHHHHHH

Sequence of entity 2 (G, H), FASTA

>5Y3D_2 viral protein genome-linked (VPg) (chains G, H)
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Primary citation

Insight Into the Interaction Between RNA Polymerase and VPg for Murine Norovirus Replication. Lee, J.H., Park, B.S., Han, K.R. et al. Front Microbiol (2018) 9:1466-1466. DOI 10.3389/fmicb.2018.01466 · 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
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…

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