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nucleocapsid_protein

Euk-Vir

Rat_arterivirus_1

nucleocapsid_protein__YP_009214666__Rat_arterivirus_1__1734441

Identity

Accession:
YP_009214666 ↗
Protein ID:
nucleocapsid_protein
Kingdom:
euk

Quality

74.3 mean pLDDT

Taxonomy

Orthornavirae› Pisuviricota› Pisoniviricetes› Nidovirales› Arteriviridae› Betaarterivirus› Rat_arterivirus_1

TaxID: 1734441

Cluster

Singleton — not in a non-trivial cluster

3D Structure

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Domains

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

D1 high residues 65-116
PDB
Domain cluster: rep: nucleocapsid_protein_N__YP_009118969__African_pouched_rat_arterivirus__1965064__D78-125
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF01481.21 best Arteri_nucleo 78.0 1.00e-21 100.0% 44.8%
CATH (36)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1p65A00 6.10.140.90 Special › Helix non-globular › Helix Hairpins › 0.94 88.0 8.51e-01 100.0% 91.2%
3uoxB01 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.74 56.0 3.52e-01 84.6% 16.3%
3u5eU00 3.30.1360.210 Alpha Beta › 2-Layer Sandwich › Gyrase A; domain 2 › 0.71 43.0 3.42e-01 90.4% 32.0%
4qmfB01 3.30.1370.10 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 › K Homology domain, type 1 0.63 38.0 3.32e-01 86.5% 37.8%
1oyiA00 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 0.63 38.0 3.56e-01 71.2% 50.0%
1f02T00 4.10.820.10 Few Secondary Structures › Irregular › Translocated Intimin Receptor; Chain T › Translocated intimin receptor, central domain 0.63 50.0 4.69e-01 90.4% 84.8%
2i2cA01 3.40.50.10330 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Probable inorganic polyphosphate/atp-NAD kinase; domain 1 0.63 47.0 3.59e-01 100.0% 34.4%
2mh9A00 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 0.61 42.0 3.24e-01 73.1% 43.3%
1kafA00 3.90.1150.20 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Transcription regulator MotA, C-terminal domain 0.61 49.0 3.81e-01 86.5% 50.0%
3znuA00 3.30.70.1060 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Dimeric alpha+beta barrel 0.61 43.0 3.46e-01 73.1% 62.8%
3vkhA08 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.59 44.0 2.74e-01 84.6% 31.3%
3cjnA00 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 0.59 48.0 3.66e-01 100.0% 76.7%
2an1D01 3.40.50.10330 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Probable inorganic polyphosphate/atp-NAD kinase; domain 1 0.58 40.0 3.01e-01 73.1% 32.3%
1s12A00 3.30.70.1490 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Cysteine protease Prp 0.58 49.0 4.04e-01 96.2% 92.6%
6ketA01 3.20.20.30 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Luciferase-like domain 0.57 44.0 2.69e-01 84.6% 92.5%
1xa3A01 3.40.50.10540 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Crotonobetainyl-coa:carnitine coa-transferase; domain 1 0.57 45.0 2.76e-01 84.6% 22.6%
3mwmA01 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 39.0 3.44e-01 80.8% 50.7%
5e1wA00 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 46.0 3.34e-01 100.0% 70.8%
1fthA00 3.90.470.20 Alpha Beta › Alpha-Beta Complex › Ribosomal Protein L22; Chain A › 4'-phosphopantetheinyl transferase domain 0.55 42.0 3.27e-01 84.6% 41.9%
3ou2A00 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.54 43.0 2.98e-01 94.2% 81.9%
1kqfA02 3.40.50.740 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.54 47.0 3.08e-01 100.0% 70.7%
4f3nA00 3.40.50.12710 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.54 46.0 2.79e-01 100.0% 19.5%
2w00A02 3.90.640.50 Alpha Beta › Alpha-Beta Complex › Actin; Chain A, domain 4 › 0.53 41.0 3.71e-01 94.2% 61.6%
1mbyA00 2.40.50.930 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.53 32.0 2.86e-01 100.0% 42.7%
4jm1A00 3.30.300.300 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › 0.53 41.0 3.55e-01 92.3% 53.6%
4r78A01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.52 35.0 2.90e-01 86.5% 38.5%
3jcmH04 3.30.70.870 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Elongation Factor G (Translational Gtpase), domain 3 0.52 44.0 3.83e-01 94.2% 75.3%
3c6fA01 3.30.240.20 Alpha Beta › 2-Layer Sandwich › CRO Repressor › bsu07140 like domains 0.52 33.0 3.13e-01 75.0% 48.4%
6lw5A01 1.20.1070.10 Mainly Alpha › Up-down Bundle › Rhopdopsin 7-helix transmembrane proteins › Rhodopsin 7-helix transmembrane proteins 0.51 44.0 2.70e-01 96.2% 15.9%
2kyyA00 3.30.950.30 Alpha Beta › 2-Layer Sandwich › Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2 › Schlafen, AAA domain 0.51 36.0 2.74e-01 100.0% 27.5%
1yt5A01 3.40.50.10330 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Probable inorganic polyphosphate/atp-NAD kinase; domain 1 0.51 42.0 3.15e-01 94.2% 36.9%
4lq0A02 3.10.28.10 Alpha Beta › Roll › Endonuclease I-creI › Homing endonucleases 0.51 38.0 2.77e-01 96.2% 28.6%
1a79A01 3.40.1350.10 Alpha Beta › 3-Layer(aba) Sandwich › Trna Endonuclease; Chain: A, domain 1 › 0.51 40.0 3.38e-01 94.2% 62.0%
1yj7B01 3.30.70.1530 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Hypothetical protein rpa1041 0.51 44.0 3.94e-01 96.2% 80.3%
3ieyB00 3.40.1350.150 Alpha Beta › 3-Layer(aba) Sandwich › Trna Endonuclease; Chain: A, domain 1 › 0.50 41.0 3.03e-01 94.2% 41.4%
1vx7X00 3.30.1360.210 Alpha Beta › 2-Layer Sandwich › Gyrase A; domain 2 › 0.50 40.0 3.48e-01 100.0% 89.7%
ECOD (52)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
7688 808.1.1.2 ↗ a+b duplicates or obligate multimers › Arterivirus nucleocapsid protein › Arterivirus nucleocapsid protein › Arterivirus nucleocapsid protein › Arteri_nucleo 0.94 88.0 8.51e-01 100.0% 91.2%
3923920 148.1.1.8 ↗ alpha arrays › Histone-like › Histone-related › Histone › TFIID_30kDa 0.71 53.0 4.29e-01 82.7% 52.4%
3399732 3016.1.1.22 ↗ 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 › PDXDC1-like_cen2 0.69 42.0 3.29e-01 86.5% 30.5%
3169604 2004.1.1.495 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › TRAPPC10_1st 0.64 40.0 2.59e-01 100.0% 14.8%
3577575 101.1.2.22 ↗ alpha arrays › HTH › HTH › winged helix domain › PCI 0.64 41.0 3.50e-01 86.5% 42.5%
3616235 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.63 40.0 3.49e-01 86.5% 42.5%
3301908 101.1.2.281 ↗ alpha arrays › HTH › HTH › winged helix domain › Tfb2 0.62 41.0 3.40e-01 71.2% 36.8%
3339574 101.1.2.385 ↗ alpha arrays › HTH › HTH › winged helix domain › HRQ1_WHD 0.60 44.0 3.82e-01 82.7% 85.6%
4024456 101.1.2.663 ↗ alpha arrays › HTH › HTH › winged helix domain › DUF7602 0.60 48.0 4.05e-01 100.0% 52.2%
3680635 101.1.2.154 ↗ alpha arrays › HTH › HTH › winged helix domain › CDT1_C 0.60 48.0 3.80e-01 100.0% 43.8%
3882687 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 0.59 49.0 2.97e-01 92.3% 19.7%
3760738 4357.1.1.9 ↗ beta barrels › WWE domain › WWE domain › WWE domain › WWE, WWE_3 0.59 46.0 3.29e-01 100.0% 29.5%
3261727 101.1.2.111 ↗ alpha arrays › HTH › HTH › winged helix domain › RQC 0.58 40.0 3.20e-01 73.1% 36.5%
3219795 5001.1.1.41 ↗ alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › 7TM_GPCR_Srw 0.58 47.0 2.89e-01 90.4% 17.3%
4325826 225.1.1.27 ↗ a+b two layers › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase-like › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase › PF26329 0.58 47.0 2.99e-01 90.4% 72.2%
3505845 101.1.2.407 ↗ alpha arrays › HTH › HTH › winged helix domain › WHD_ORC2 0.58 40.0 3.35e-01 75.0% 85.0%
2966548 4964.1.1.0 ↗ alpha arrays › helical bundle in Bacillus stearothermophilus-like DNA polymerase I › helical bundle in Bacillus stearothermophilus-like DNA polymerase I › helical bundle in Bacillus stearothermophilus-like DNA polymerase I 0.57 47.0 3.29e-01 94.2% 69.4%
4043003 601.7.1.6 ↗ alpha bundles › Four-helical up-and-down bundle › HEPN › Nucleotidyltransferase substrate binding subunit/domain › GlnD_UR_UTase 0.57 48.0 3.32e-01 92.3% 34.7%
3383404 101.1.2.154 ↗ alpha arrays › HTH › HTH › winged helix domain › CDT1_C 0.57 47.0 3.76e-01 98.1% 46.2%
4649222 101.1.2.15 ↗ alpha arrays › HTH › HTH › winged helix domain › MarR 0.56 49.0 3.71e-01 100.0% 98.5%
3467284 101.1.2.154 ↗ alpha arrays › HTH › HTH › winged helix domain › CDT1_C 0.56 45.0 3.57e-01 94.2% 42.6%
3487912 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.56 48.0 3.79e-01 98.1% 45.5%
3261151 109.3.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › Ankyrin repeat › Ankyrin repeat 0.56 41.0 2.54e-01 100.0% 13.6%
4172732 7527.1.1.2 ↗ a/b three-layered sandwiches › SurE-like/CoA-transferase family III (CaiB/BaiF) › SurE-like/CoA-transferase family III (CaiB/BaiF) › SurE-like/CoA-transferase family III (CaiB/BaiF) › CoA_transf_3 0.56 43.0 2.52e-01 82.7% 17.5%
1176726 4325.1.1.2 ↗ mixed a+b and a/b › YegP-like › YegP-like › YegP-like › P53_C 0.55 43.0 3.90e-01 100.0% 62.0%
3773033 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 44.0 2.68e-01 98.1% 12.8%
4014614 223.1.1.24 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › PAS_8 0.55 45.0 3.35e-01 96.2% 40.0%
3981752 829.1.1.1 ↗ a+b duplicates or obligate multimers › NinB › NinB › NinB › NinB 0.55 41.0 3.15e-01 84.6% 52.3%
3795771 5054.1.1.8 ↗ alpha complex topology › Voltage-gated ion channels › Voltage-gated ion channels › Voltage-gated ion channels › Ion_trans_2 0.55 44.0 2.66e-01 90.4% 12.5%
3686916 2484.1.1.2 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Actin 0.54 45.0 3.08e-01 100.0% 78.6%
3726808 4163.1.1.1 ↗ alpha bundles › GINS helical bundle-like › GINS helical bundle-like › PSF1 N-terminal domain-like › Sld5 0.54 44.0 3.20e-01 98.1% 35.0%
3520913 5054.1.1.8 ↗ alpha complex topology › Voltage-gated ion channels › Voltage-gated ion channels › Voltage-gated ion channels › Ion_trans_2 0.54 46.0 2.63e-01 98.1% 48.9%
3611776 5086.1.1.0 ↗ alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins 0.54 41.0 3.16e-01 90.4% 49.3%
3210565 101.1.2.267 ↗ alpha arrays › HTH › HTH › winged helix domain › Nse4_C 0.53 46.0 3.32e-01 96.2% 91.0%
5056642 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.53 39.0 3.35e-01 84.6% 82.7%
3799214 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.53 46.0 3.50e-01 94.2% 46.1%
3587282 142.1.1.10 ↗ alpha complex topology › Sigma2 domain-like › Sigma2 domain of RNA polymerase sigma factors › Sigma2 domain of RNA polymerase sigma factors › HTH_16 0.53 40.0 3.76e-01 88.5% 75.7%
3573598 101.1.2.154 ↗ alpha arrays › HTH › HTH › winged helix domain › CDT1_C 0.53 44.0 3.47e-01 100.0% 44.5%
3735563 101.1.2.267 ↗ alpha arrays › HTH › HTH › winged helix domain › Nse4_C 0.52 47.0 3.34e-01 98.1% 86.7%
3997731 304.24.1.0 ↗ a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like 0.52 44.0 3.85e-01 94.2% 72.5%
3940660 3343.1.1.2 ↗ alpha complex topology › gamma-tubulin complex protein 4 (GCP4) › gamma-tubulin complex protein 4 (GCP4) › gamma-tubulin complex protein 4 (GCP4) › GCP_C_terminal,GCP_N_terminal 0.52 42.0 2.42e-01 100.0% 7.9%
3679669 101.1.2.267 ↗ alpha arrays › HTH › HTH › winged helix domain › Nse4_C 0.52 43.0 3.38e-01 92.3% 73.6%
3390936 101.1.2.267 ↗ alpha arrays › HTH › HTH › winged helix domain › Nse4_C 0.52 44.0 3.54e-01 94.2% 51.0%
3574069 604.12.1.62 ↗ alpha bundles › Spectrin repeat-like › MIT domain › MIT domain › DuoxA 0.52 46.0 3.48e-01 100.0% 61.6%
3743466 101.1.2.267 ↗ alpha arrays › HTH › HTH › winged helix domain › Nse4_C 0.52 42.0 3.40e-01 92.3% 78.1%
3584644 304.9.1.59 ↗ a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD › CEBP_ZZ 0.51 35.0 2.86e-01 92.3% 34.5%
3541293 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.51 39.0 3.39e-01 88.5% 97.8%
3287925 101.1.2.15 ↗ alpha arrays › HTH › HTH › winged helix domain › MarR 0.51 40.0 3.05e-01 98.1% 75.5%
3938116 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 0.50 42.0 2.65e-01 90.4% 34.9%
4922053 5093.1.1.4 ↗ a+b complex topology › Head and neck region of the ectodomain of paramyxoviruses fusion glycoprotein › Head and neck region of the ectodomain of paramyxoviruses fusion glycoprotein › Head and neck region of the ectodomain of paramyxoviruses fusion glycoprotein › Fusion_gly, Fibritin_C 0.50 43.0 2.55e-01 100.0% 18.4%
3743565 109.4.1.313 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › UTP20_N 0.50 40.0 2.55e-01 94.2% 27.5%
3611700 3755.3.1.0 ↗ alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin 0.50 42.0 2.70e-01 98.1% 18.0%