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RNA-dependent_RNA_polymerase

Euk-Vir

Crimson_clover_cryptic_virus_2

RNA-dependent_RNA_polymerase__YP_009508059__Crimson_clover_cryptic_virus_2__1323528

Identity

Accession:
YP_009508059 ↗
Protein ID:
RNA-dependent_RNA_polymerase
Kingdom:
euk

Quality

73.7 mean pLDDT

Taxonomy

Orthornavirae› Pisuviricota› Duplopiviricetes› Durnavirales› Partitiviridae› Betapartitivirus› Crimson_clover_cryptic_virus_2

TaxID: 1323528

Cluster

View cluster (450 members)

3D Structure

Download PDB Download Scores JSON

Domains

high = three domain segmentations agree, medium = two domain segmentations agree. Numbered high-first then medium, N→C within each tier.

D1 medium residues 102-124_158-380_412-492_718-742
PDB
Domain cluster: representative
ECOD (1)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
217141 304.48.1.15 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RdRP_3 0.67 51.0 5.12e-01 92.0% 76.2%
D2 medium residues 381-411_493-525
PDB
Domain cluster: representative
D3 medium residues 526-589
PDB
Domain cluster: rep: RNA-dependent_RNA_polymerase__YP_007889825__Hop_trefoil_cryptic_virus_2__1323523__D516-583
D4 medium residues 590-649
PDB
Domain cluster: representative
CATH (50)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4a25B01 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.80 70.0 5.10e-01 98.3% 87.6%
2clbA01 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.79 68.0 4.99e-01 96.7% 91.8%
1urfA00 1.10.287.160 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HR1 repeat 0.77 53.0 4.77e-01 71.7% 61.7%
2yjkC00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.76 66.0 4.90e-01 98.3% 90.4%
2ondA00 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.76 62.0 3.94e-01 93.3% 22.1%
1ugoA00 1.20.58.120 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › BAG domain 0.75 63.0 5.33e-01 93.3% 77.8%
5hayA02 1.25.40.440 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Nucleoporin, helical domain, central subdomain 0.74 61.0 5.59e-01 90.0% 70.9%
2pusA04 6.10.140.300 Special › Helix non-globular › Helix Hairpins › 0.74 66.0 5.39e-01 100.0% 65.7%
2d2sA01 1.20.58.1210 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Exo84p, N-terminal helical domain 0.73 64.0 5.20e-01 100.0% 64.7%
3mzkB03 1.20.58.940 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.72 47.0 4.46e-01 83.3% 57.1%
2lhrA00 1.20.58.1270 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.71 61.0 5.65e-01 100.0% 75.6%
2i6hA02 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.70 52.0 4.54e-01 90.0% 51.0%
1vf7A03 1.10.287.470 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.70 48.0 4.84e-01 71.7% 88.3%
3k1hA00 3.30.1120.180 Alpha Beta › 2-Layer Sandwich › Arylsulfatase, C-terminal domain › Flagellar FLiS export co-chaperone, HP1076 0.70 53.0 4.26e-01 81.7% 100.0%
1x9bA00 1.20.58.290 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Hypothetical membrane protein ta0354_69_121. 0.69 52.0 5.44e-01 86.7% 92.5%
8ek4A01 1.20.120.20 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Apolipoprotein 0.69 59.0 4.60e-01 96.7% 88.7%
2b5dX01 3.20.110.10 Alpha Beta › Alpha-Beta Barrel › 7-stranded beta/alpha barrel › Glycoside hydrolase 38, N terminal domain 0.69 49.0 2.94e-01 75.0% 24.5%
4gpkB01 1.25.40.1000 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.69 55.0 4.75e-01 91.7% 58.6%
2qkdA02 2.60.120.1040 Mainly Beta › Sandwich › Jelly Rolls › ZPR1, A/B domain 0.69 49.0 3.78e-01 76.7% 39.3%
2guzA00 1.10.287.110 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › DnaJ domain 0.68 53.0 5.02e-01 85.0% 76.1%
3zilA00 1.25.10.60 Mainly Alpha › Alpha Horseshoe › Leucine-rich Repeat Variant › Rad61, Wapl domain 0.68 52.0 3.18e-01 83.3% 28.5%
3qwwA03 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.68 56.0 3.97e-01 93.3% 31.9%
6fndA01 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.67 55.0 3.90e-01 91.7% 36.6%
2gomA00 1.10.10.1270 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Sbi, C3 binding domain IV 0.66 54.0 5.43e-01 95.0% 95.1%
1nklA00 1.10.225.10 Mainly Alpha › Orthogonal Bundle › NK-Lysin › Saposin-like 0.66 49.0 4.52e-01 81.7% 66.7%
1sumB02 1.20.58.220 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphate transport system protein phou homolog 2; domain 2 0.66 53.0 4.35e-01 93.3% 76.3%
3ujpB01 3.40.50.1980 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Nitrogenase molybdenum iron protein domain 0.65 54.0 4.15e-01 95.0% 97.3%
2ra1A03 1.20.58.770 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.65 51.0 5.09e-01 90.0% 98.4%
2juaA00 1.20.1480.30 Mainly Alpha › Up-down Bundle › hypothetical protein mp506/mpn330, domain 1 › Designed four-helix bundle protein 0.65 51.0 4.43e-01 91.7% 74.5%
5tqbB01 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.64 54.0 3.47e-01 100.0% 38.6%
3s63A00 1.10.225.10 Mainly Alpha › Orthogonal Bundle › NK-Lysin › Saposin-like 0.63 47.0 4.20e-01 81.7% 58.0%
2wzkA03 1.20.1310.10 Mainly Alpha › Up-down Bundle › 5 helical Cullin repeat like › Cullin Repeats 0.63 46.0 3.88e-01 81.7% 59.1%
1m62A00 1.20.58.120 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › BAG domain 0.63 51.0 4.67e-01 98.3% 92.0%
2nrlA00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.63 51.0 3.91e-01 91.7% 93.8%
2mx8A01 1.10.274.70 Mainly Alpha › Orthogonal Bundle › Enzyme I; Chain A, domain 2 › Spidroin, N-terminal domain 0.62 48.0 3.95e-01 85.0% 68.1%
3kd4A02 3.10.620.30 Alpha Beta › Roll › C8orf32 fold › 0.62 48.0 3.60e-01 86.7% 68.1%
1sxjD03 1.20.272.10 Mainly Alpha › Up-down Bundle › Zinc Finger, Delta Prime; domain 3 › 0.61 47.0 4.14e-01 85.0% 95.6%
1ux8A00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.61 47.0 3.94e-01 90.0% 92.4%
2y39A00 1.20.120.1490 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.60 45.0 3.79e-01 83.3% 90.0%
2ctqA01 1.10.287.110 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › DnaJ domain 0.59 43.0 3.76e-01 78.3% 54.3%
2gwcA00 3.30.590.20 Alpha Beta › 2-Layer Sandwich › Creatine Kinase; Chain A, domain 2 › 0.59 47.0 2.84e-01 90.0% 88.6%
4ks9A01 1.20.140.90 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Malonyl-CoA decarboxylase, oligemerization domain 0.59 42.0 3.43e-01 78.3% 57.1%
4hehA01 1.10.1240.10 Mainly Alpha › Orthogonal Bundle › Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 › Methionine synthase domain 0.59 46.0 4.16e-01 86.7% 85.5%
2ygwA01 1.20.140.90 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Malonyl-CoA decarboxylase, oligemerization domain 0.58 46.0 3.55e-01 91.7% 69.9%
4hyqA00 3.40.50.1110 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › SGNH hydrolase 0.58 49.0 3.26e-01 93.3% 33.9%
4uurA00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.58 45.0 3.72e-01 91.7% 88.7%
1iomA01 1.10.580.10 Mainly Alpha › Orthogonal Bundle › Citrate Synthase; domain 1 › Citrate Synthase, domain 1 0.57 44.0 3.05e-01 90.0% 62.8%
3a7rA02 3.30.390.50 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › CO dehydrogenase flavoprotein, C-terminal domain 0.57 41.0 3.78e-01 88.3% 56.2%
1dk8A02 1.10.167.10 Mainly Alpha › Orthogonal Bundle › Regulator of G-protein Signalling 4; domain 2 › Regulator of G-protein Signalling 4, domain 2 0.56 43.0 3.96e-01 90.0% 77.6%
2ogwA01 3.40.50.1980 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Nitrogenase molybdenum iron protein domain 0.54 41.0 3.29e-01 91.7% 97.3%
ECOD (45)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3796824 109.7.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › Cytochrome c oxidase subunit E › Cytochrome c oxidase subunit E 0.81 69.0 6.58e-01 93.3% 87.1%
3575524 109.4.1.777 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.79 66.0 4.07e-01 91.7% 17.9%
4595635 148.1.3.26 ↗ alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain › AAA_lid_9 0.79 54.0 3.90e-01 71.7% 29.4%
3940186 226.1.1.0 ↗ a+b two layers › POZ domain › POZ domain › POZ domain 0.78 67.0 6.11e-01 96.7% 81.2%
3695244 3615.1.1.0 ↗ alpha bundles › Bacterial dynamin-like protein helical domain › Bacterial dynamin-like protein helical domain › Bacterial dynamin-like protein helical domain 0.77 64.0 4.61e-01 91.7% 34.1%
4949691 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.77 65.0 4.73e-01 95.0% 33.5%
3277865 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.77 65.0 4.98e-01 93.3% 43.0%
3515234 109.3.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › Ankyrin repeat › Ankyrin repeat 0.76 65.0 4.91e-01 95.0% 49.7%
3938380 604.12.1.0 ↗ alpha bundles › Spectrin repeat-like › MIT domain › MIT domain 0.76 66.0 6.13e-01 96.7% 85.3%
4999446 109.4.1.198 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_12 0.76 63.0 4.04e-01 91.7% 21.2%
4928363 150.1.1.1 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin › Ferritin 0.75 65.0 5.07e-01 96.7% 90.6%
4024049 1134.1.1.0 ↗ alpha bundles › C-terminal helical domain of alanine-tRNA ligase › C-terminal helical domain of alanine-tRNA ligase › Eukaryotic C-Ala helical domain 0.75 62.0 5.77e-01 91.7% 93.3%
3930551 109.4.1.1304 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_8, TPR_10, TPR_12 0.75 62.0 3.85e-01 91.7% 17.7%
3703921 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.75 61.0 3.55e-01 90.0% 17.9%
3517181 109.4.1.1286 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_8, TPR_12 0.75 61.0 4.67e-01 93.3% 43.4%
4970859 601.28.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › VPS28 C-terminal domain-like › VPS28 C-terminal domain-like 0.74 63.0 5.32e-01 95.0% 63.0%
3606255 109.4.1.238 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › SRP_TPR_like 0.74 59.0 4.25e-01 86.7% 33.3%
3232479 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.74 61.0 4.43e-01 93.3% 34.9%
3834057 109.4.1.585 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › DUF627 0.74 58.0 3.53e-01 83.3% 17.7%
3232863 109.4.1.192 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_8 0.74 61.0 3.81e-01 93.3% 26.5%
3969284 633.28.1.2 ↗ alpha bundles › Bromodomain-like › Tsi6 › Tsi6 › DUF4404 0.73 59.0 5.35e-01 88.3% 77.5%
5001522 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.72 62.0 5.20e-01 96.7% 99.0%
4401167 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.72 57.0 4.54e-01 88.3% 45.6%
3606126 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.72 59.0 4.06e-01 91.7% 27.1%
3620341 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.71 59.0 4.99e-01 95.0% 58.1%
3313027 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.71 60.0 3.97e-01 96.7% 40.4%
3497121 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.71 58.0 4.92e-01 90.0% 99.0%
3598441 109.4.1.1200 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_WDR35 0.71 58.0 4.97e-01 90.0% 69.5%
3399891 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.71 58.0 3.95e-01 90.0% 28.2%
3177396 109.4.1.237 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Wap1 0.70 57.0 3.45e-01 90.0% 27.3%
3628771 109.4.1.1923 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › HAT_Syf1_CNRKL1_C, HAT_PRP39_C 0.70 58.0 4.10e-01 93.3% 32.1%
3976607 604.34.1.1 ↗ alpha bundles › Spectrin repeat-like › Helical bundle domain in arginine decarboxylase › Helical bundle domain in arginine decarboxylase › Arg_decarb_HB 0.70 60.0 5.11e-01 98.3% 77.0%
3597915 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.69 57.0 3.72e-01 93.3% 21.4%
3580280 604.1.1.192 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › PF26998 0.69 59.0 5.15e-01 100.0% 95.8%
3935024 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.68 57.0 4.27e-01 96.7% 41.2%
3421659 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.68 58.0 4.03e-01 98.3% 38.1%
3973478 131.1.1.12 ↗ alpha complex topology › PDEase-like › HD-domain/PDEase-like › HD-domain/PDEase-like › HD_4 0.68 54.0 3.92e-01 90.0% 34.1%
3627089 198.1.1.0 ↗ alpha arrays › Saposin-like › Saposin-like › Saposin-like 0.68 51.0 4.72e-01 83.3% 67.5%
3391259 604.6.1.0 ↗ alpha bundles › Spectrin repeat-like › GAT-like domain › GAT-like domain 0.68 57.0 5.07e-01 98.3% 86.7%
3456183 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.67 56.0 4.83e-01 96.7% 77.0%
4969867 109.2.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › alpha/alpha toroid › alpha/alpha toroid 0.67 57.0 3.57e-01 100.0% 20.0%
3531345 109.4.1.498 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › DUF4487 0.66 58.0 4.08e-01 100.0% 50.3%
3939155 109.4.1.3 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Arm,Arm_3 0.62 50.0 3.43e-01 95.0% 27.1%
3243671 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.61 44.0 3.89e-01 76.7% 63.3%
3268013 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.61 52.0 3.72e-01 100.0% 38.0%