8C1N: FMDV 3D polymerase

FMDV 3D polymerase in complex with 3B1 protein solved in P212121 space group. Determined by X-ray diffraction at 1.7 Å resolution. Released 26 Apr 2023.

Method: X-ray diffraction
Resolution: 1.7 Å
Organism: Foot-and-mouth disease virus
Chains: 3
Atoms: 8,308
Mol. weight: 112.57 kDa
Ligands: 3PO
Released: 26 Apr 2023

Explore 8C1N in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8C1N contains 55 α-helices and 50 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: 26 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	2-13	12	1
β-strand	21-23	3	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	128-130	3
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
β-strand	323-324	2	8
β-strand	332-336	5	6
β-strand	339-344	6	6
α-helix	351-353	3
α-helix	354-358	5
β-strand	364-366	3	7
β-strand	384-385	2	9
β-strand	388-392	5	9
β-strand	399-402	4	9
α-helix	405-412	8
β-strand	414-416	3	2
α-helix	420-431	12
α-helix	432-434	3
α-helix	436-443	8
α-helix	444-446	3
α-helix	455-473	19

Chain B: 28 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	10
β-strand	21-23	3	11
α-helix	26-30	5
β-strand	34-36	3	12
α-helix	37-38	2
α-helix	47	1
α-helix	52-55	4
α-helix	64-67	4
α-helix	68-89	22
α-helix	94-97	4
α-helix	98-103	6
β-strand	105	1	13
β-strand	108	1	13
α-helix	109-112	4
α-helix	121-124	4
α-helix	128-130	3
β-strand	132-133	2	14
β-strand	138-139	2	14
α-helix	141-151	11
β-strand	159-163	5	10
β-strand	167-169	3	12
α-helix	170-174	5
β-strand	180-183	4	10
α-helix	186-205	20
β-strand	208	1	15
β-strand	213	1	15
α-helix	219-230	12
β-strand	235-241	7	15
α-helix	250-260	11
α-helix	263-265	3
α-helix	270-276	7
β-strand	280-285	6	10
β-strand	288-293	6	10
α-helix	303-322	20
β-strand	323	1	16
β-strand	332-336	5	15
β-strand	339-344	6	15
α-helix	350-353	4
α-helix	354-358	5
β-strand	364-366	3	15
β-strand	385	1	17
β-strand	388-392	5	17
β-strand	399-403	5	17
α-helix	405-412	8
β-strand	414-416	3	11
α-helix	420-431	12
α-helix	432-434	3
α-helix	436-443	8
α-helix	444-446	3
β-strand	447	1	18
β-strand	450	1	18
α-helix	451-454	4
α-helix	455-468	14

Chain C: 1 helix, 2 β-strands

Element	Residues	Length	Sheet
β-strand	7-8	2	8
β-strand	17	1	16
α-helix	18-19	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
RNA-directed RNA polymerase 3D-POL	A, B	protein	481	Foot-and-mouth disease virus	P03311
Protein 3B-1	C	protein	23	Foot-and-mouth disease virus	P03311

Sequence of entity 1 (A, B), FASTA

>8C1N_1 RNA-directed RNA polymerase 3D-POL (chains A, B)
GLIVDTRDVEERVHVMRKTKLAPTVAHGVFNPEFGPAALSNKDPRLNEGVVLDEVIFSKH
KGDTKMSAEDKALFRRCAADYASRLHSVLGTANAPLSIYEAIKGVDGLDAMEPDTAPGLP
WALQGKRRGALIDFENGTVGPEVEAALKLMEKREYKFACQTFLKDEIRPMEKVRAGKTRI
VDVLPVEHILYTRMMIGRFCAQMHSNNGPQIGSAVGCNPDVDWQRFGTHFAQYRNVWDVD
YSAFDANHCSDAMNIMFEEVFRTEFGFHPNAEWILKTLVNTEHAYENKRITVEGGMPSGC
SATSIINTILNNIYVLYALRRHYEGVELDTYTMISYGDDIVVASDYDLDFEALKPHFKSL
GQTITPADKSDKGFVLGHSITDVTFLKRHFHMDYGTGFYKPVMASKTLEAILSFARRGTI
QEKLISVAGLAVHSGPDEYRRLFEPFQGLFEIPSYRSLYLRWVNAVCGDAAAAKEHHHHH
H

Sequence of entity 2 (C), FASTA

>8C1N_2 Protein 3B-1 (chains C)
GPYAGPLERQRPLKVRAKLPRQE

Ligands and cofactors

ID	Name	Formula	Copies
3PO	Triphosphate	H5 O10 P3	2

Water and common crystallization additives (GOL, ACT) are not listed.

Primary citation

Dual role of the foot-and-mouth disease virus 3B1 protein in the replication complex: As protein primer and as an essential component to recruit 3Dpol to membranes. Ferrer-Orta, C., Ferrero, D.S., Verdaguer, N. PLoS Pathog (2023) 19:e1011373-e1011373. DOI 10.1371/journal.ppat.1011373 · PubMed

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

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
6GVY 2.2 Å, Mutant M16A of RNA dependent RNA polymerase 3D from Foot-and-Mouth 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

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