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RNA-dependent_RNA_polymerase

Euk-Vir

Hop_trefoil_cryptic_virus_2

RNA-dependent_RNA_polymerase__YP_007889825__Hop_trefoil_cryptic_virus_2__1323523

Identity

Accession:
YP_007889825 ↗
Protein ID:
RNA-dependent_RNA_polymerase
Kingdom:
euk

Quality

71.6 mean pLDDT

Taxonomy

Orthornavirae› Pisuviricota› Duplopiviricetes› Durnavirales› Partitiviridae› Betapartitivirus› Hop_trefoil_cryptic_virus_2

TaxID: 1323523

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 high residues 516-583
PDB
Domain cluster: representative
CATH (32)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1cjaA02 1.10.1070.11 Mainly Alpha › Orthogonal Bundle › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, Domain 5 › Phosphatidylinositol 3-/4-kinase, catalytic domain 0.65 46.0 3.47e-01 76.5% 85.3%
4kyzA00 3.30.70.600 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ribosomal protein S10 0.64 49.0 3.71e-01 83.8% 34.1%
4alzA03 3.30.70.1770 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.61 45.0 4.68e-01 83.8% 84.4%
1zcdA00 1.20.1530.10 Mainly Alpha › Up-down Bundle › Na+/H+ antiporter like fold › Na+/H+ antiporter like domain 0.60 44.0 2.85e-01 82.4% 74.5%
3u1nB01 1.10.3210.10 Mainly Alpha › Orthogonal Bundle › Hypothetical protein af1432 › Hypothetical protein af1432 0.60 50.0 3.32e-01 100.0% 60.7%
3w6kC00 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.60 44.0 4.05e-01 77.9% 73.6%
6gpxB00 1.20.1070.10 Mainly Alpha › Up-down Bundle › Rhopdopsin 7-helix transmembrane proteins › Rhodopsin 7-helix transmembrane proteins 0.59 40.0 2.75e-01 72.1% 56.7%
1cnzA00 3.40.718.10 Alpha Beta › 3-Layer(aba) Sandwich › Isopropylmalate Dehydrogenase › Isopropylmalate Dehydrogenase 0.59 42.0 2.68e-01 76.5% 17.9%
1i72A00 3.60.90.10 Alpha Beta › 4-Layer Sandwich › S-adenosylmethionine decarboxylase › S-adenosylmethionine decarboxylase 0.58 46.0 3.20e-01 89.7% 83.7%
2v7kA02 1.20.58.480 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.58 44.0 3.15e-01 82.4% 91.1%
2f1rA00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.58 43.0 3.36e-01 79.4% 62.8%
2xrfC00 3.40.50.1580 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Nucleoside phosphorylase domain 0.58 48.0 3.24e-01 97.1% 73.8%
2f7aA01 3.40.190.10 Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II 0.57 41.0 3.50e-01 77.9% 88.4%
5fmgG00 3.60.20.10 Alpha Beta › 4-Layer Sandwich › Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 › Aminohydrolase, N-terminal nucleophile (Ntn) domain 0.57 46.0 3.25e-01 91.2% 67.6%
6c1qB02 1.20.1070.10 Mainly Alpha › Up-down Bundle › Rhopdopsin 7-helix transmembrane proteins › Rhodopsin 7-helix transmembrane proteins 0.56 43.0 2.89e-01 83.8% 79.6%
4gcvC00 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.56 40.0 3.17e-01 76.5% 44.7%
1ucrB00 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.56 40.0 3.90e-01 76.5% 80.0%
5ucoA02 3.40.47.10 Alpha Beta › 3-Layer(aba) Sandwich › Peroxisomal Thiolase; Chain A, domain 1 › Thiolase/Chalcone synthase 0.55 41.0 3.26e-01 80.9% 49.7%
2qx2A00 3.10.570.10 Alpha Beta › Roll › sex pheromone staph- cam373 precursor fold › sex pheromone staph- cam373 precursor domain 0.55 49.0 3.18e-01 100.0% 41.5%
3l09A02 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.55 40.0 3.72e-01 76.5% 77.4%
2wshA00 3.40.1440.40 Alpha Beta › 3-Layer(aba) Sandwich › GIY-YIG endonuclease › 0.55 38.0 3.07e-01 72.1% 62.7%
3df8A00 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.54 39.0 3.38e-01 76.5% 54.1%
1nigA00 1.20.1200.10 Mainly Alpha › Up-down Bundle › Hypothetical Protein Ta1238; Chain: A; › Cobalamin adenosyltransferase-like 0.54 40.0 3.29e-01 83.8% 81.5%
2z86D02 3.90.550.10 Alpha Beta › Alpha-Beta Complex › Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A › Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A 0.54 38.0 2.64e-01 76.5% 31.2%
8dvhB01 3.30.230.10 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S5; domain 2 › 0.54 44.0 3.35e-01 95.6% 51.4%
4blpB00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.53 43.0 2.91e-01 91.2% 79.6%
2rdpA00 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.53 38.0 3.07e-01 77.9% 50.0%
1xjcA00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.53 39.0 3.11e-01 79.4% 72.9%
7q5yB01 3.30.460.80 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › NADH:ubiquinone oxidoreductase Nqo5 subunit 0.52 39.0 3.37e-01 83.8% 65.0%
2hqbA02 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.52 39.0 3.03e-01 80.9% 46.7%
1s12A00 3.30.70.1490 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Cysteine protease Prp 0.51 38.0 3.46e-01 80.9% 92.6%
3pqkA00 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.50 36.0 3.26e-01 77.9% 56.6%
ECOD (39)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4635290 4967.1.1.25 ↗ alpha bundles › helical bundle domain in reverse transcriptase-like polymerases › helical bundle domain in reverse transcriptase-like polymerases › helical bundle domain in reverse transcriptase-like polymerases › Intron_maturas2+MatK_N 0.76 66.0 4.06e-01 100.0% 20.5%
4088089 304.48.1.39 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › MatK_N 0.74 65.0 4.22e-01 100.0% 22.3%
3226369 2004.1.2.1 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › PEP carboxykinase catalytic C-terminal domain › PEPCK_GTP 0.66 49.0 3.21e-01 79.4% 61.4%
4543273 304.36.1.1 ↗ a+b two layers › Alpha-beta plaits › YajQ-like › YajQ-like › DUF520 0.65 45.0 4.58e-01 79.4% 75.4%
4598960 304.36.1.0 ↗ a+b two layers › Alpha-beta plaits › YajQ-like › YajQ-like 0.65 46.0 4.59e-01 80.9% 72.9%
5058517 186.1.1.0 ↗ alpha arrays › lambda integrase-N-like › lambda integrase-N › lambda integrase-N 0.63 48.0 4.01e-01 80.9% 84.2%
3927940 304.36.1.2 ↗ a+b two layers › Alpha-beta plaits › YajQ-like › YajQ-like › RVT_1 0.63 52.0 4.69e-01 100.0% 67.6%
3935908 304.48.1.1 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 0.63 53.0 4.49e-01 100.0% 54.4%
5016606 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.62 40.0 3.30e-01 75.0% 32.9%
4935046 2004.1.1.97 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › MobB 0.61 46.0 3.72e-01 80.9% 83.8%
4649054 3016.1.1.0 ↗ a+b two layers › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases 0.59 41.0 3.68e-01 89.7% 50.5%
3675128 304.9.1.20 ↗ a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD › RRM_8 0.59 44.0 4.44e-01 83.8% 84.3%
5018003 4040.1.1.1 ↗ alpha bundles › Fic-like › Fic-like › Fic-like › Fic 0.58 44.0 2.91e-01 82.4% 74.4%
3816635 219.1.1.79 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › Transglut_core2 0.58 43.0 3.29e-01 77.9% 75.3%
4990309 150.2.1.1 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Cobalamin adenosyltransferase › Cobalamin adenosyltransferase › Cob_adeno_trans 0.58 43.0 3.26e-01 77.9% 70.9%
3440733 7581.1.1.6 ↗ a/b three-layered sandwiches › Thiolase-like › Thiolase-like › Thiolase-like › Chal_sti_synt_C 0.57 41.0 3.16e-01 77.9% 44.4%
4939406 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.57 41.0 3.08e-01 76.5% 35.4%
5032275 101.1.2.15 ↗ alpha arrays › HTH › HTH › winged helix domain › MarR 0.56 40.0 3.51e-01 75.0% 65.0%
5029625 7546.1.1.1 ↗ a/b three-layered sandwiches › Glutaminase/Asparaginase N-terminal domain › Glutaminase/Asparaginase N-terminal domain › Glutaminase/Asparaginase N-terminal domain › Asparaginase 0.56 45.0 3.25e-01 92.6% 68.9%
5031078 101.1.2.48 ↗ alpha arrays › HTH › HTH › winged helix domain › PadR 0.55 39.0 3.48e-01 75.0% 69.0%
4295958 5001.1.1.1 ↗ alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › 7tm_1 0.55 40.0 2.91e-01 77.9% 45.0%
5038360 2006.1.1.11 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › HAD-like › Hydrolase_3 0.55 42.0 2.90e-01 83.8% 50.6%
4068860 101.1.2.54 ↗ alpha arrays › HTH › HTH › winged helix domain › Penicillinase_R 0.54 37.0 3.12e-01 72.1% 50.0%
4934384 101.1.2.947 ↗ alpha arrays › HTH › HTH › winged helix domain › PF27234 0.54 38.0 3.65e-01 77.9% 100.0%
4946762 7573.1.1.1 ↗ a/b three-layered sandwiches › PRTase-like › PRTase-like › PRTase-like › Pribosyltran 0.54 41.0 3.05e-01 83.8% 64.1%
3437543 2485.1.1.43 ↗ a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like › Thioredoxin_6 0.54 40.0 3.34e-01 80.9% 45.0%
4986692 2004.1.1.97 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › MobB 0.53 39.0 3.12e-01 77.9% 57.1%
3281567 101.1.2.26 ↗ alpha arrays › HTH › HTH › winged helix domain › HxlR 0.53 39.0 3.17e-01 76.5% 45.6%
3198423 5000.6.1.0 ↗ alpha arrays › Toxins' membrane translocation domains › Tethering factor for nuclear proteasome cut8 › Tethering factor for nuclear proteasome cut8 0.53 39.0 2.75e-01 98.5% 25.2%
4243508 101.1.2.14 ↗ alpha arrays › HTH › HTH › winged helix domain › HTH_5 0.53 39.0 3.37e-01 77.9% 53.3%
3482807 277.1.1.0 ↗ a+b two layers › PX domain › PX domain › PX domain 0.53 42.0 3.58e-01 85.3% 65.7%
3980816 3261.1.1.0 ↗ a+b two layers › amino-terminal domain of OmpATb › amino-terminal domain of OmpATb › amino-terminal domain of OmpATb 0.52 38.0 3.76e-01 91.2% 73.3%
5070280 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.52 38.0 3.42e-01 77.9% 58.9%
5061454 316.1.1.0 ↗ a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase 0.52 44.0 3.48e-01 100.0% 84.4%
3206500 7510.1.1.1 ↗ a/b three-layered sandwiches › Isocitrate/Isopropylmalate dehydrogenase-like › Isocitrate/Isopropylmalate dehydrogenase-like › Isocitrate/Isopropylmalate dehydrogenase-like › Iso_dh 0.51 42.0 3.33e-01 98.5% 97.0%
4603837 264.1.1.15 ↗ beta barrels › LigT-like › LigT-related › LigT-related › DUF1045 0.51 42.0 3.08e-01 95.6% 75.8%
4995140 2484.1.1.124 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › OrfB_IS605 0.51 42.0 3.27e-01 89.7% 93.8%
4857877 5001.1.1.1 ↗ alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › 7tm_1 0.51 43.0 3.23e-01 95.6% 64.2%
4298539 2500.1.1.2 ↗ a/b barrels › Ten stranded beta/alpha barrel › Ten stranded beta/alpha barrel › Ten stranded beta/alpha barrel › Ribonuc_red_lgC 0.51 40.0 2.43e-01 89.7% 54.4%
D2 high residues 586-688
PDB
Domain cluster: rep: RNA-dependent_RNA_polymerase__YP_007889823__Red_clover_cryptic_virus_2__1323524__D588-687
D3 medium residues 87-124_148-199_334-365
PDB
Domain cluster: rep: putative_RNA-dependent_RNA_polymerase__YP_003104768__Primula_malacoides_virus_China_Mar2007__479713__D102-183_314-331
D4 medium residues 200-243_317-333_366-498_718-737
PDB
Domain cluster: rep: RNA-dependent_RNA_polymerase__YP_009293586__Cannabis_cryptic_virus__1115692__D183-262_410-474_493-506_711-739
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00680.26 best RdRP_1 26.2 4.80e-06 67.3% 25.1%
D5 medium residues 244-316
PDB