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RNA-dependent_RNA_polymerase

Euk-Vir

Wenling_narna-like_virus_9

RNA-dependent_RNA_polymerase__YP_009337200__Wenling_narna-like_virus_9__1923509

Identity

Accession:
YP_009337200 ↗
Protein ID:
RNA-dependent_RNA_polymerase
Kingdom:
euk

Quality

66.5 mean pLDDT

Cluster

Singleton — not in a non-trivial cluster

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 561-644
PDB
D2 medium residues 43-169
PDB
Domain cluster: representative
CATH (19)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
7vwtA01 1.10.600.10 Mainly Alpha › Orthogonal Bundle › Farnesyl Diphosphate Synthase › Farnesyl Diphosphate Synthase 0.70 48.0 3.58e-01 79.5% 28.6%
2z16B01 1.20.91.10 Mainly Alpha › Up-down Bundle › Influenza Virus Matrix Protein; Chain A, domain 1 › Influenza matrix M1, N-terminal subdomain 1 0.63 37.0 4.39e-01 96.9% 91.0%
2iw3A02 1.20.1390.20 Mainly Alpha › Up-down Bundle › PWI domain › 0.60 42.0 4.77e-01 100.0% 100.0%
6i3mE01 1.20.120.420 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › translation initiation factor eif-2b, domain 1 0.60 34.0 3.31e-01 81.9% 49.6%
1abvA00 1.10.520.20 Mainly Alpha › Orthogonal Bundle › Peroxidase; domain 1 › N-terminal domain of the delta subunit of the F1F0-ATP synthase 0.57 43.0 4.61e-01 80.3% 94.3%
5cy5B00 1.20.1200.10 Mainly Alpha › Up-down Bundle › Hypothetical Protein Ta1238; Chain: A; › Cobalamin adenosyltransferase-like 0.57 46.0 4.38e-01 100.0% 73.2%
3ezhA00 1.20.120.960 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Histidine kinase NarX, sensor domain 0.57 36.0 3.80e-01 85.8% 70.2%
1m2vB01 1.20.120.730 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Sec23/Sec24 helical domain 0.57 43.0 3.93e-01 85.0% 59.8%
1puoB00 1.20.920.50 Mainly Alpha › Up-down Bundle › Histone Acetyltransferase; Chain A › 0.55 46.0 4.49e-01 94.5% 99.3%
7ae2A01 1.20.120.580 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › bsu32300-like 0.53 30.0 2.94e-01 82.7% 48.2%
1xg2B00 1.20.140.40 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Invertase/pectin methylesterase inhibitor family protein 0.53 44.0 4.23e-01 100.0% 77.5%
3a11B01 1.20.120.420 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › translation initiation factor eif-2b, domain 1 0.52 41.0 4.14e-01 81.1% 89.6%
1sj8A02 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.52 45.0 4.66e-01 98.4% 100.0%
3kyiA00 1.20.120.160 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › HPT domain 0.52 41.0 4.16e-01 83.5% 97.7%
3jyhA02 1.20.120.980 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Serine carboxypeptidase S28, SKS domain 0.51 38.0 3.65e-01 78.0% 91.3%
7zdtD01 1.20.1560.10 Mainly Alpha › Up-down Bundle › ABC transporter transmembrane region fold › ABC transporter type 1, transmembrane domain 0.51 46.0 3.41e-01 99.2% 96.6%
1wdzA00 1.20.1270.60 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Arfaptin homology (AH) domain/BAR domain 0.51 41.0 3.30e-01 84.3% 84.8%
2p7vA00 1.20.120.1370 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Regulator of RNA polymerase sigma(70) subunit, domain 4 0.51 38.0 3.62e-01 87.4% 66.2%
1x04A00 1.20.1270.60 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Arfaptin homology (AH) domain/BAR domain 0.50 40.0 3.44e-01 84.3% 86.5%
ECOD (29)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
1487362 3930.2.1.1 ↗ alpha bundles › Helical bundle insertion in helicase domains › Helical bundle in endoribonuclease Dicer › Helical bundle in endoribonuclease Dicer › Dicer_PBD 0.72 52.0 5.38e-01 97.6% 79.0%
3516004 2004.1.1.30 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Helicase_C 0.69 54.0 4.00e-01 100.0% 33.8%
4015729 192.7.1.0 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm 0.66 40.0 4.08e-01 100.0% 60.8%
3629324 2003.1.1.0 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains 0.66 39.0 4.26e-01 78.0% 70.5%
4602904 6091.1.1.0 ↗ alpha bundles › Helical bundle domain in Endo-alpha-N-acetylgalactosaminidase › Helical bundle domain in Endo-alpha-N-acetylgalactosaminidase › Helical bundle domain in Endo-alpha-N-acetylgalactosaminidase 0.64 35.0 4.21e-01 89.0% 80.0%
4809777 6004.1.1.2 ↗ extended segments › FATC domain › FATC domain › FATC domain › ETC_C1_NDUFA5 0.64 35.0 3.77e-01 94.5% 62.4%
3971690 601.3.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › Histidine-containing phosphotransfer domain, HPT domain › Histidine-containing phosphotransfer domain, HPT domain 0.63 38.0 3.84e-01 86.6% 60.0%
3988434 633.2.1.0 ↗ alpha bundles › Bromodomain-like › Carnobacteriocin B2 immunity protein › Carnobacteriocin B2 immunity protein 0.62 45.0 4.88e-01 98.4% 90.4%
4854386 6004.1.1.2 ↗ extended segments › FATC domain › FATC domain › FATC domain › ETC_C1_NDUFA5 0.62 34.0 3.80e-01 93.7% 66.7%
4318541 4006.1.1.1 ↗ alpha bundles › Release factor (Pfam 00472) N-terminal alpha helical domain › Release factor (Pfam 00472) N-terminal alpha helical domain › Release factor (Pfam 00472) N-terminal alpha helical domain › PCRF 0.62 30.0 3.24e-01 96.9% 53.3%
3782668 604.5.1.16 ↗ alpha bundles › Spectrin repeat-like › PhoU-like (Pfam 01895) › PhoU-like (Pfam 01895) › ArAE_2_N 0.61 48.0 3.89e-01 84.3% 80.0%
3272953 3930.1.1.0 ↗ alpha bundles › Helical bundle insertion in helicase domains › Helical bundle in Hef helicase › Helical bundle in Hef helicase 0.58 54.0 5.24e-01 99.2% 97.9%
3833909 633.4.1.1 ↗ alpha bundles › Bromodomain-like › Plant invertase/pectin methylesterase inhibitor › Plant invertase/pectin methylesterase inhibitor › PMEI 0.56 44.0 4.31e-01 100.0% 77.5%
3800481 174.1.1.0 ↗ few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain 0.55 48.0 4.54e-01 100.0% 79.3%
3377179 601.1.2.0 ↗ alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › I/LWEQ domain (Pfam 01608) 0.55 43.0 3.75e-01 83.5% 92.5%
3384541 174.1.1.0 ↗ few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain 0.54 48.0 4.48e-01 100.0% 78.1%
3814234 633.4.1.1 ↗ alpha bundles › Bromodomain-like › Plant invertase/pectin methylesterase inhibitor › Plant invertase/pectin methylesterase inhibitor › PMEI 0.54 43.0 4.30e-01 100.0% 84.6%
2755028 6004.1.1.2 ↗ extended segments › FATC domain › FATC domain › FATC domain › ETC_C1_NDUFA5 0.53 34.0 3.64e-01 96.1% 72.2%
3228302 601.1.2.0 ↗ alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › I/LWEQ domain (Pfam 01608) 0.52 45.0 4.61e-01 99.2% 100.0%
3924971 174.1.1.0 ↗ few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain 0.52 47.0 4.43e-01 100.0% 87.6%
3629560 150.1.1.0 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin 0.51 46.0 4.34e-01 100.0% 87.7%
3242640 174.1.1.0 ↗ few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain 0.51 46.0 4.19e-01 100.0% 78.0%
None — 0.51 39.0 2.89e-01 84.3% 28.4%
3337031 3755.3.1.0 ↗ alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin 0.51 39.0 3.50e-01 81.1% 68.9%
3176858 174.1.1.0 ↗ few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain 0.51 46.0 4.46e-01 100.0% 92.1%
3628162 5073.1.1.0 ↗ alpha bundles › Calcium ATPase transmembrane domain-related › Calcium ATPase transmembrane domain-related › Calcium ATPase transmembrane domain M 0.50 46.0 3.13e-01 100.0% 29.7%
3194757 3276.1.1.0 ↗ alpha arrays › N-terminal domain in MogR repressor › N-terminal domain in MogR repressor › N-terminal domain in MogR repressor 0.50 36.0 3.74e-01 91.3% 80.9%
4682191 4177.1.1.0 ↗ alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like 0.50 40.0 3.22e-01 85.0% 89.5%
3541710 5050.1.1.10 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › MFS_2 0.50 46.0 3.57e-01 100.0% 81.5%
D3 medium residues 209-361_407-448
PDB
Domain cluster: rep: RNA_dependent_RNA_polymerase__YP_005352912__Clitocybe_odora_virus__1162083__D188-234_322-366_403-448
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF05919.17 best Mitovir_RNA_pol 46.3 4.60e-12 70.8% 22.3%
CATH (7)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3hiuD00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.55 40.0 4.40e-01 94.9% 94.1%
2k3iA01 3.30.70.860 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.52 25.0 3.46e-01 95.4% 96.5%
1mukA02 3.90.1850.10 Alpha Beta › Alpha-Beta Complex › RNA-directed RNA polymerase lambda-3 › RNA-directed RNA polymerase lambda-3 0.52 48.0 3.51e-01 100.0% 48.4%
2jzxA02 3.30.1370.10 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 › K Homology domain, type 1 0.52 23.0 3.30e-01 93.3% 96.2%
1k8kA04 3.90.640.10 Alpha Beta › Alpha-Beta Complex › Actin; Chain A, domain 4 › ATPase, substrate binding domain, subdomain 4 0.51 19.0 2.67e-01 86.2% 66.3%
2nugB02 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.51 19.0 2.94e-01 77.4% 87.3%
8sbeA02 1.20.1250.20 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › MFS general substrate transporter like domains 0.50 36.0 3.68e-01 71.8% 95.7%
ECOD (11)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4002132 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 0.53 39.0 3.34e-01 76.9% 56.0%
4004424 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 0.52 49.0 3.87e-01 100.0% 57.1%
3923013 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 0.52 46.0 3.80e-01 94.9% 58.3%
3589612 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 0.52 49.0 4.04e-01 100.0% 64.8%
5368 304.48.1.23 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RdRP_5 0.52 48.0 3.78e-01 100.0% 62.4%
3327074 5001.1.1.122 ↗ alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › PF27754 0.51 38.0 3.29e-01 75.4% 54.2%
3794245 5001.1.1.5 ↗ alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › 7tm_3 0.51 35.0 3.46e-01 73.3% 63.8%
3173834 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 0.51 48.0 3.69e-01 100.0% 49.5%
3792091 304.48.1.25 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RRM_4 0.51 46.0 3.73e-01 100.0% 53.6%
4152428 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 0.51 45.0 3.68e-01 95.4% 56.9%
223786 304.48.1.16 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RdRP_4 0.50 46.0 3.90e-01 100.0% 66.6%
D4 medium residues 362-406_449-538
PDB
Domain cluster: rep: RNA-dependent_RNA_polymerase__YP_009272901__Fusarium_poae_mitovirus_4__1848153__D300-342_409-485
Pfam (2)
AccessionNameScoreE-valueQ covHMM cov
PF05919.17 best Mitovir_RNA_pol 93.1 2.80e-26 66.7% 17.3%
PF05919.17 Mitovir_RNA_pol 44.2 2.00e-11 35.6% 8.8%
D5 medium residues 781-837
PDB