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RNA-dependant_RNA_polymerase

Euk-Vir

Tellina_virus_1

RNA-dependant_RNA_polymerase__YP_009508102__Tellina_virus_1__321302

Identity

Accession:
YP_009508102 ↗
Protein ID:
RNA-dependant_RNA_polymerase
Kingdom:
euk

Quality

65.5 mean pLDDT

Taxonomy

Orthornavirae› Birnaviridae› Telnavirus› Tellina_virus_1

TaxID: 321302

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 615-689
PDB
D2 medium residues 43-74_101-118
PDB
D3 medium residues 193-220_232-245_304-350_412-480
PDB
Domain cluster: rep: VP1_RNA-dependent_RNA_polymerase__NP_690839__Infectious_bursal_disease_virus__10995__D189-259_308-337_421-491
Pfam (2)
AccessionNameScoreE-valueQ covHMM cov
PF04197.18 best Birna_RdRp_palm 74.0 1.70e-20 48.1% 13.0%
PF04197.18 Birna_RdRp_palm 42.5 6.20e-11 34.2% 8.8%
CATH (4)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2pggA01 3.90.1730.10 Alpha Beta › Alpha-Beta Complex › Infectious bursal virus vp1 polymerase fold › Infectious bursal virus vp1 polymerase domain 0.92 87.0 6.45e-01 97.5% 67.6%
2r7rA05 1.10.357.80 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › 0.64 59.0 5.67e-01 99.4% 94.9%
1mvfD00 2.10.260.10 Mainly Beta › Ribbon › Pemi-like Protein 1; Chain: D › 0.55 18.0 3.20e-01 73.4% 100.0%
1d0xA04 1.20.120.720 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Myosin VI head, motor domain, U50 subdomain 0.51 27.0 2.95e-01 86.1% 58.4%
ECOD (17)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
1145898 304.48.2.1 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › 'palm' domain in birnaviruse RNA-dependent RNA polymerase › Birna_RdRp_palm 0.94 92.0 6.08e-01 100.0% 55.6%
None — 0.94 91.0 6.10e-01 100.0% 56.9%
2994348 304.48.1.9 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RdRP_1,CoV_RPol_N 0.73 69.0 4.17e-01 100.0% 23.8%
2541763 304.48.1.8 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RdRP_1 0.71 66.0 4.95e-01 100.0% 63.5%
None — 0.69 65.0 4.84e-01 100.0% 60.7%
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 0.69 64.0 4.85e-01 100.0% 62.7%
4014158 304.48.1.0 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like 0.68 49.0 3.91e-01 73.4% 54.6%
4296494 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 0.68 48.0 3.85e-01 73.4% 56.1%
3669721 304.48.1.0 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like 0.67 48.0 3.88e-01 73.4% 67.0%
3465998 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 0.66 47.0 3.82e-01 73.4% 53.4%
4188583 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 0.62 57.0 4.19e-01 100.0% 53.5%
5018583 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 0.61 52.0 4.11e-01 90.5% 64.4%
3899435 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 0.61 55.0 4.03e-01 100.0% 53.5%
5001967 1.1.3.2 ↗ beta barrels › cradle loop barrel › RIFT-related › AbrB › MazE_antitoxin 0.56 18.0 3.21e-01 73.4% 90.0%
4079860 101.1.10.0 ↗ alpha arrays › HTH › HTH › Cyclin-like 0.53 21.0 3.24e-01 98.7% 93.3%
1299892 101.1.2.88 ↗ alpha arrays › HTH › HTH › winged helix domain › Dimerisation 0.51 25.0 2.88e-01 73.4% 59.6%
4411694 3018.1.1.1 ↗ a+b two layers › MesJ substrate recognition domain-like › MesJ substrate recognition domain-like › MesJ substrate recognition domain-like › TilS 0.50 29.0 3.63e-01 99.4% 97.8%
D4 medium residues 221-231_246-303
PDB
Domain cluster: representative
CATH (9)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4oydB00 1.10.132.20 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › Ribosome-recycling factor 0.76 57.0 4.75e-01 79.7% 71.8%
2l37A00 6.10.250.890 Special › Helix non-globular › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.72 44.0 5.41e-01 78.3% 100.0%
2odmA00 1.10.287.750 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › SO2669-like 0.72 51.0 4.85e-01 81.2% 64.6%
2k0nA00 1.10.246.20 Mainly Alpha › Orthogonal Bundle › Serum Albumin; Chain A, Domain 1 › Coactivator CBP, KIX domain 0.67 51.0 4.76e-01 82.6% 65.9%
2ffjA01 1.10.8.380 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Uncharacterised protein PF01937, DUF89, domain 1 0.63 39.0 4.23e-01 81.2% 75.0%
1x4tA01 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.62 42.0 4.54e-01 71.0% 84.5%
2yqyA00 1.20.120.450 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › dinb family like domain 0.61 48.0 3.89e-01 84.1% 81.0%
1ufvA02 3.30.1300.10 Alpha Beta › 2-Layer Sandwich › Pantoate--beta-alanine Ligase; Chain: A,domain 2 › Pantoate-beta-alanine ligase, C-terminal domain 0.57 49.0 4.41e-01 98.6% 88.9%
4a18Q01 1.10.10.1760 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Ribosomal protein L36 0.54 34.0 3.49e-01 98.6% 63.8%
ECOD (24)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3538309 1128.1.1.1 ↗ alpha bundles › LYR protein › LYR protein › LYR protein › Complex1_LYR 0.83 56.0 5.33e-01 71.0% 60.0%
3734404 1128.1.1.1 ↗ alpha bundles › LYR protein › LYR protein › LYR protein › Complex1_LYR 0.78 55.0 5.25e-01 84.1% 63.7%
3483522 101.35.1.0 ↗ alpha arrays › HTH › DNA repair regulatory protein RecX › DNA repair regulatory protein RecX 0.78 55.0 4.18e-01 73.9% 71.3%
3839762 1008.1.1.0 ↗ alpha bundles › BRCC36 C-terminal helical domain › BRCC36 C-terminal helical domain › BRCC36 C-terminal helical domain 0.77 54.0 5.06e-01 73.9% 60.0%
3328865 3788.1.1.0 ↗ alpha bundles › Viral accessory protein x (Vpx) / viral protein r (Vpr) › Viral accessory protein x (Vpx) / viral protein r (Vpr) › Viral accessory protein x (Vpx) / viral protein r (Vpr) 0.74 54.0 5.40e-01 78.3% 74.3%
4117096 5054.1.1.2 ↗ alpha complex topology › Voltage-gated ion channels › Voltage-gated ion channels › Voltage-gated ion channels › Ion_trans 0.71 52.0 3.71e-01 76.8% 32.1%
4033044 632.19.1.3 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Choline binding protein A › Choline binding protein A › DUF1542 0.71 49.0 4.85e-01 81.2% 68.0%
4031187 632.19.1.3 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Choline binding protein A › Choline binding protein A › DUF1542 0.71 49.0 4.79e-01 81.2% 66.7%
4034220 632.2.1.5 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Bacterial immunoglobulin/albumin-binding domains › Bacterial immunoglobulin/albumin-binding domains › DUF1542 0.71 52.0 5.21e-01 79.7% 77.1%
4033051 632.19.1.3 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Choline binding protein A › Choline binding protein A › DUF1542 0.70 51.0 5.16e-01 81.2% 78.6%
4031489 632.19.1.3 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Choline binding protein A › Choline binding protein A › DUF1542 0.69 51.0 4.98e-01 81.2% 72.0%
4033046 632.19.1.3 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Choline binding protein A › Choline binding protein A › DUF1542 0.69 52.0 5.06e-01 84.1% 74.7%
4034571 632.19.1.3 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Choline binding protein A › Choline binding protein A › DUF1542 0.67 49.0 4.85e-01 81.2% 73.3%
3437328 632.10.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Coronavirus NSP7-like › Coronavirus NSP7-like 0.65 43.0 4.77e-01 98.6% 87.3%
3963735 5069.1.3.1 ↗ alpha bundles › Transmembrane heme-binding four-helical bundle › Transmembrane heme-binding four-helical bundle › Fumarate reductase respiratory complex transmembrane subunits › Sdh_cyt 0.64 56.0 4.82e-01 100.0% 82.3%
3981475 3636.1.1.0 ↗ a+b two layers › XPD arch domain › XPD arch domain › XPD arch domain 0.63 46.0 3.72e-01 78.3% 39.3%
4113180 108.1.1.0 ↗ alpha arrays › EF-hand › EF-hand-related › EF-hand 0.63 46.0 3.70e-01 79.7% 72.9%
3180179 148.1.1.15 ↗ alpha arrays › Histone-like › Histone-related › Histone › CENP-X 0.61 52.0 5.03e-01 91.3% 100.0%
3714091 632.11.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like 0.60 44.0 4.33e-01 84.1% 72.0%
5078788 604.12.1.0 ↗ alpha bundles › Spectrin repeat-like › MIT domain › MIT domain 0.57 49.0 4.51e-01 95.7% 84.4%
4952741 148.1.1.0 ↗ alpha arrays › Histone-like › Histone-related › Histone 0.56 45.0 4.08e-01 91.3% 69.0%
4941939 148.1.1.4 ↗ alpha arrays › Histone-like › Histone-related › Histone › CBFD_NFYB_HMF 0.55 46.0 4.14e-01 91.3% 72.6%
3228717 103.4.1.1 ↗ alpha arrays › RuvA-C › Elongation factor TFIIS domain 2/ Kix domain of creb binding protein › Elongation factor TFIIS domain 2/ Kix domain of creb binding protein › KIX 0.54 46.0 4.52e-01 94.2% 88.0%
4940509 2498.1.1.0 ↗ mixed a+b and a/b › Zincin-like › "Metalloproteases (""zincins"") catalytic domain" › "Metalloproteases (""zincins"") catalytic domain" 0.51 43.0 3.88e-01 95.7% 70.0%
D5 medium residues 351-411_544-614
PDB
Domain cluster: rep: VP1_protein__YP_009177609__Tasmanian_aquabirnavirus__1721090__D358-396_515-582
Pfam (2)
AccessionNameScoreE-valueQ covHMM cov
PF20488.4 best Birna_VP1_thumb 45.7 9.00e-12 52.3% 38.9%
PF04197.18 Birna_RdRp_palm 50.9 1.70e-13 51.5% 10.5%
D6 medium residues 481-543
PDB
Domain cluster: representative
CATH (4)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2datA00 1.20.920.10 Mainly Alpha › Up-down Bundle › Histone Acetyltransferase; Chain A › Bromodomain-like 0.58 46.0 3.73e-01 88.9% 87.8%
1u7kA00 1.10.375.10 Mainly Alpha › Orthogonal Bundle › Human Immunodeficiency Virus Type 1 Capsid Protein › Human Immunodeficiency Virus Type 1 Capsid Protein 0.56 42.0 3.44e-01 84.1% 71.0%
1lr0A00 3.30.1150.10 Alpha Beta › 2-Layer Sandwich › Fusion Protein Consisting Of Minor Coat Protein, Glycine Rich Linker, Tola, And A His Tag; Chain: A; Domain 2 › 0.53 47.0 3.78e-01 100.0% 73.0%
4wojA02 3.30.360.10 Alpha Beta › 2-Layer Sandwich › Dihydrodipicolinate Reductase; domain 2 › Dihydrodipicolinate Reductase; domain 2 0.53 44.0 3.10e-01 98.4% 28.3%
ECOD (5)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4489725 306.7.1.1 ↗ a+b two layers › Glucose permease domain IIB-like › Trigger factor ribosome-binding domain › Trigger factor ribosome-binding domain › Trigger_N 0.61 40.0 3.29e-01 88.9% 36.5%
4508255 306.7.1.1 ↗ a+b two layers › Glucose permease domain IIB-like › Trigger factor ribosome-binding domain › Trigger factor ribosome-binding domain › Trigger_N 0.58 47.0 3.89e-01 92.1% 70.0%
4522938 306.7.1.1 ↗ a+b two layers › Glucose permease domain IIB-like › Trigger factor ribosome-binding domain › Trigger factor ribosome-binding domain › Trigger_N 0.58 48.0 3.92e-01 93.7% 89.2%
4291138 306.7.1.1 ↗ a+b two layers › Glucose permease domain IIB-like › Trigger factor ribosome-binding domain › Trigger factor ribosome-binding domain › Trigger_N 0.57 46.0 3.76e-01 92.1% 67.2%
3651005 306.7.1.1 ↗ a+b two layers › Glucose permease domain IIB-like › Trigger factor ribosome-binding domain › Trigger factor ribosome-binding domain › Trigger_N 0.55 45.0 3.90e-01 95.2% 68.6%
D7 medium residues 723-753_770-826
PDB