6GVY: Genome polyprotein

Mutant M16A of RNA dependent RNA polymerase 3D from Foot-and-Mouth disease Virus complexed with an template -primer RNA. Determined by X-ray diffraction at 2.2 Å resolution. Released 1 Aug 2018.

Method: X-ray diffraction
Resolution: 2.2 Å
Organisms: Foot-and-mouth disease virus - type C, synthetic construct
Chains: 3
Atoms: 4,031
Mol. weight: 58.26 kDa
Released: 1 Aug 2018

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

Secondary structure: helices and β-sheets

6GVY contains 29 α-helices and 23 β-strands across 1 chain. 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, 23 β-strands

Element	Residues	Length	Sheet
β-strand	2-5	4	1
β-strand	8-13	6	1
β-strand	22-23	2	2
α-helix	27-30	4
β-strand	34-36	3	3
α-helix	37-38	2
α-helix	47	1
α-helix	52-55	4
α-helix	68-89	22
α-helix	94-97	4
α-helix	98-103	6
β-strand	105	1	4
β-strand	108	1	4
α-helix	109-112	4
α-helix	121-123	3
α-helix	128-131	4
β-strand	132-133	2	5
β-strand	138-139	2	5
α-helix	141-151	11
β-strand	159-163	5	1
β-strand	167-169	3	3
α-helix	170-174	5
β-strand	180-183	4	1
α-helix	184-185	2
α-helix	186-205	20
β-strand	208	1	6
β-strand	213	1	6
α-helix	219-230	12
β-strand	235-238	4	6
β-strand	239-241	3	7
α-helix	250-260	11
α-helix	263-265	3
α-helix	270-276	7
β-strand	280-293	14	1
α-helix	303-322	20
α-helix	328-330	3
β-strand	332-336	5	6
β-strand	339-344	6	6
α-helix	350-358	9
β-strand	364-366	3	7
α-helix	380-382	3
β-strand	384-385	2	8
β-strand	388-393	6	8
β-strand	398-402	5	8
α-helix	403-404	2
α-helix	405-413	9
β-strand	414-415	2	2
α-helix	420-431	12
α-helix	432-434	3
α-helix	436-443	8
α-helix	444-446	3
α-helix	455-465	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Genome polyprotein	A	protein	481	Foot-and-mouth disease virus - type C	P03311
RNA (5'-r(pcpcpgpgp*g)-3')	B	RNA	5	synthetic construct
RNA (5'-r(pcpupcpcpcpgpgpg)-3')	C	RNA	8	synthetic construct

Sequence of entity 1 (A), FASTA

>6GVY_1 Genome polyprotein (chains A)
GLIVDTRDVEERVHVARKTKLAPTVAHGVFNPEFGPAALSNKDPRLNEGVVLDEVIFSKH
KGDTKMSAEDKALFRRCAADYASRLHSVLGTANAPLSIYEAIKGVDGLDAMEPDTAPGLP
WALQGKRRGALIDFENGTVGPEVEAALKLMEKREYKFACQTFLKDEIRPMEKVRAGKTRI
VDVLPVEHILYTRMMIGRFCAQMHSNNGPQIGSAVGCNPDVDWQRFGTHFAQYRNVWDVD
YSAFDANHCSDAMNIMFEEVFRTEFGFHPNAEWILKTLVNTEHAYENKRITVEGGMPSGC
SATSIINTILNNIYVLYALRRHYEGVELDTYTMISYGDDIVVASDYDLDFEALKPHFKSL
GQTITPADKSDKGFVLGHSITDVTFLKRHFHMDYGTGFYKPVMASKTLEAILSFARRGTI
QEKLISVAGLAVHSGPDEYRRLFEPFQGLFEIPSYRSLYLRWVNAVCGDAAAALEHHHHH
H

Sequence of entity 2 (B), FASTA

>6GVY_2 RNA (5'-R(P*CP*CP*GP*GP*G)-3') (chains B)
CCGGG

Sequence of entity 3 (C), FASTA

>6GVY_3 RNA (5'-R(P*CP*UP*CP*CP*CP*GP*GP*G)-3') (chains C)
CUCCCGGG

Primary citation

Contribution of a Multifunctional Polymerase Region of Foot-and-Mouth Disease Virus to Lethal Mutagenesis. de la Higuera, I., Ferrer-Orta, C., Moreno, E. et al. J Virol (2018) 92. DOI 10.1128/JVI.01119-18 · PubMed

Other PDB entries of the same protein (UniProt P03311), best resolution first:

8C1N 1.7 Å, FMDV 3D polymerase in complex with 3B1 protein solved in P212121 space group
4WYW 1.8 Å, Mutant K20E of 3D polymerase from Foot-and-Mouth Disease Virus
6KWL 1.8 Å, Crystal structure of pSLA-1*0401(R156A) complex with FMDV-derived epitope MTAHITVPY
8C2P 1.85 Å, FMDV 3D polymerase in complex with 3B3
4WYL 2.0 Å, Mutant K18E of 3D polymerase from Foot-and-Moth Disease Virus
6S2L 2.3 Å, FMDV 3D polymerase crystallized in presence of (F)uridylylated VPg peptide
6GVV 2.35 Å, Mutant M16A of RNA dependent RNA polymerase 3D from Foot-and-Mouth disease Virus
5N8X 2.4 Å, Trigonal structure of mutant V173I of 3D polymerase from Foot-and-Mouth Disease Virus
6KWK 2.5 Å, Crystal structure of pSLA-1*0401 complex with FMDV-derived epitope MTAHITVPY
9I3H 2.5 Å, CP of RHDV mutant - N15
4WZM 2.52 Å, Mutant K18E of RNA dependent RNA polymerase from Foot-and-Mouth Disease Virus complexed…
5N95 2.6 Å, Tetragonal structure of mutant V173I of 3D polymerase from Foot-and-Mouth Disease Virus

Browse structure collections

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