←Back to structures

DNA-dependent_RNA_polymerase_II_second_largestsubunit

Euk-Vir

Bohle_iridovirus

DNA-dependent_RNA_polymerase_II_second_largestsubunit__YP_009506723__Bohle_iridovirus__100220

Identity

Accession:: YP_009506723 ↗
Protein ID:: DNA-dependent_RNA_polymerase_II_second_largestsubunit
Kingdom:: euk

Quality

73.5 mean pLDDT

Taxonomy

Bamfordvirae› Nucleocytoviricota› Megaviricetes› Pimascovirales› Iridoviridae› Ranavirus› Bohle_iridovirus

TaxID: 100220

Cluster

View cluster (58 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 838-887_920-981

PDB

Domain cluster: rep: putative_RNA_polymerase_beta_subunit__YP_009052296__Aureococcus_anophagefferens_virus__1474867__D765-873

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF00562.34 best	RNA_pol_Rpb2_6	29.2	7.20e-07	100.0%	31.1%

D2 medium residues 572-671_706-729

PDB

Domain cluster: rep: RNA_polymerase_beta_subunit__YP_010087885__Lymphocystis_disease_virus_4__2704413__D444-546

CATH (1)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
6iw6A02	3.30.460.10	Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › Beta Polymerase, domain 2	0.51	37.0	3.96e-01	83.1%	86.1%

ECOD (14)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
3637895	4961.1.1.1 ↗	a+b complex topology › inserted a+b domain in yeast RNA polymerase beta subunit › inserted a+b domain in yeast RNA polymerase beta subunit › inserted a+b domain in yeast RNA polymerase beta subunit › RNA_pol_Rpb2_4	0.83	58.0	6.63e-01	71.8%	95.8%
3231491	4961.1.1.1 ↗	a+b complex topology › inserted a+b domain in yeast RNA polymerase beta subunit › inserted a+b domain in yeast RNA polymerase beta subunit › inserted a+b domain in yeast RNA polymerase beta subunit › RNA_pol_Rpb2_4	0.82	57.0	6.53e-01	71.8%	95.8%
5062681	4961.1.1.1 ↗	a+b complex topology › inserted a+b domain in yeast RNA polymerase beta subunit › inserted a+b domain in yeast RNA polymerase beta subunit › inserted a+b domain in yeast RNA polymerase beta subunit › RNA_pol_Rpb2_4	0.81	54.0	6.49e-01	71.0%	98.8%
4979469	4961.1.1.0 ↗	a+b complex topology › inserted a+b domain in yeast RNA polymerase beta subunit › inserted a+b domain in yeast RNA polymerase beta subunit › inserted a+b domain in yeast RNA polymerase beta subunit	0.80	55.0	6.46e-01	71.0%	96.7%
5073048	4961.1.1.1 ↗	a+b complex topology › inserted a+b domain in yeast RNA polymerase beta subunit › inserted a+b domain in yeast RNA polymerase beta subunit › inserted a+b domain in yeast RNA polymerase beta subunit › RNA_pol_Rpb2_4	0.79	55.0	6.44e-01	70.2%	96.7%
4939951	4961.1.1.1 ↗	a+b complex topology › inserted a+b domain in yeast RNA polymerase beta subunit › inserted a+b domain in yeast RNA polymerase beta subunit › inserted a+b domain in yeast RNA polymerase beta subunit › RNA_pol_Rpb2_4	0.79	54.0	6.16e-01	70.2%	97.9%
4927222	4961.1.1.1 ↗	a+b complex topology › inserted a+b domain in yeast RNA polymerase beta subunit › inserted a+b domain in yeast RNA polymerase beta subunit › inserted a+b domain in yeast RNA polymerase beta subunit › RNA_pol_Rpb2_4	0.79	54.0	6.21e-01	70.2%	96.8%
3654329	4961.1.1.1 ↗	a+b complex topology › inserted a+b domain in yeast RNA polymerase beta subunit › inserted a+b domain in yeast RNA polymerase beta subunit › inserted a+b domain in yeast RNA polymerase beta subunit › RNA_pol_Rpb2_4	0.78	54.0	6.28e-01	71.0%	96.7%
4935989	4961.1.1.1 ↗	a+b complex topology › inserted a+b domain in yeast RNA polymerase beta subunit › inserted a+b domain in yeast RNA polymerase beta subunit › inserted a+b domain in yeast RNA polymerase beta subunit › RNA_pol_Rpb2_4	0.77	53.0	6.14e-01	70.2%	97.8%
4948672	4961.1.1.1 ↗	a+b complex topology › inserted a+b domain in yeast RNA polymerase beta subunit › inserted a+b domain in yeast RNA polymerase beta subunit › inserted a+b domain in yeast RNA polymerase beta subunit › RNA_pol_Rpb2_4	0.76	60.0	5.69e-01	81.5%	87.4%
3922689	4961.1.1.2 ↗	a+b complex topology › inserted a+b domain in yeast RNA polymerase beta subunit › inserted a+b domain in yeast RNA polymerase beta subunit › inserted a+b domain in yeast RNA polymerase beta subunit › RNA_pol_Rpa2_4	0.75	52.0	5.72e-01	70.2%	98.0%
4855745	4961.1.1.1 ↗	a+b complex topology › inserted a+b domain in yeast RNA polymerase beta subunit › inserted a+b domain in yeast RNA polymerase beta subunit › inserted a+b domain in yeast RNA polymerase beta subunit › RNA_pol_Rpb2_4	0.74	58.0	6.44e-01	90.3%	100.0%
3492372	4961.1.1.2 ↗	a+b complex topology › inserted a+b domain in yeast RNA polymerase beta subunit › inserted a+b domain in yeast RNA polymerase beta subunit › inserted a+b domain in yeast RNA polymerase beta subunit › RNA_pol_Rpa2_4	0.74	51.0	5.40e-01	70.2%	97.3%
4028533	325.1.8.1 ↗	a+b complex topology › alpha/beta-Hammerhead/Barrel-sandwich hybrid › alpha/beta-Hammerhead/Barrel-sandwich hybrid › Ribosomal L27 protein › Ribosomal_L27	0.51	36.0	3.74e-01	88.7%	75.0%

D3 medium residues 730-791

PDB

Domain cluster: rep: DNA-dependent_RNA_polymerase_II_second_largest_subunit_domain_6,7,3,2_beta_subunit__YP_031641__Frog_virus_3__10493__D740-806

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF00562.34 best	RNA_pol_Rpb2_6	48.0	1.40e-12	90.3%	14.8%

D4 medium residues 792-835_983-1118

PDB

Domain cluster: rep: KU935715.1__AND75470.1__ME3_309__00309__D264-326_420-534

Pfam (2)

Accession	Name	Score	E-value	Q cov	HMM cov
PF00562.34 best	RNA_pol_Rpb2_6	174.6	5.00e-51	76.1%	37.0%
PF00562.34	RNA_pol_Rpb2_6	33.6	3.30e-08	25.0%	11.5%

D5 medium residues 1119-1212

PDB