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nucleocapsid_protein

Euk-Vir

Xapuri_virus

nucleocapsid_protein__YP_010086247__Xapuri_virus__2267561

Identity

Accession:
YP_010086247 ↗
Protein ID:
nucleocapsid_protein
Kingdom:
euk

Quality

79.5 mean pLDDT

Taxonomy

Orthornavirae› Negarnaviricota› Bunyaviricetes› Hareavirales› Arenaviridae› Mammarenavirus› Xapuri_virus

TaxID: 2267561

Cluster

View cluster (26 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 356-547
PDB
Domain cluster: rep: nucleoprotein__YP_010086252__Dante_Muikkunen_virus_1__2447916__D386-583
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF17290.9 best Arena_ncap_C 261.4 4.30e-78 92.2% 95.0%
D2 medium residues 7-27_84-117_256-330
PDB
Domain cluster: rep: nucleoprotein__YP_006590087__CAS_virus__1223561__D1-21_80-113_255-329
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00843.23 best Arena_nucleocap 132.4 2.70e-38 60.0% 22.8%
D3 medium residues 28-83_162-190
PDB
Domain cluster: representative
Pfam (2)
AccessionNameScoreE-valueQ covHMM cov
PF00843.23 best Arena_nucleocap 68.2 9.10e-19 72.9% 18.0%
PF00843.23 Arena_nucleocap 32.9 4.60e-08 36.5% 8.7%
CATH (13)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4exjA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.62 45.0 3.98e-01 75.3% 90.1%
4wzxA01 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.58 39.0 4.15e-01 71.8% 78.7%
3o39A00 1.20.120.1490 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.57 41.0 3.97e-01 75.3% 94.8%
2rpaA00 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.56 36.0 3.83e-01 71.8% 72.7%
2hsnA02 1.20.1050.110 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.54 38.0 3.60e-01 72.9% 74.8%
3efzB00 1.20.190.20 Mainly Alpha › Up-down Bundle › Delta-Endotoxin; domain 1 › 14-3-3 domain 0.54 40.0 3.05e-01 80.0% 65.3%
3q5dA02 1.20.58.420 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › AHSP 0.54 40.0 3.88e-01 80.0% 78.4%
1vw4801 1.10.1200.10 Mainly Alpha › Orthogonal Bundle › Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A › ACP-like 0.54 39.0 4.18e-01 82.4% 90.4%
6xxvC00 1.10.132.20 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › Ribosome-recycling factor 0.53 40.0 3.64e-01 78.8% 86.5%
3f2eA00 1.20.58.800 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.53 36.0 3.64e-01 88.2% 71.1%
3c7jA02 1.20.120.530 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › GntR ligand-binding domain-like 0.52 41.0 3.56e-01 88.2% 64.4%
4epzA00 1.25.40.810 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › UpxZ 0.51 38.0 3.20e-01 82.4% 55.2%
6wfqC01 1.20.120.530 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › GntR ligand-binding domain-like 0.50 44.0 3.74e-01 98.8% 67.6%
ECOD (9)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
406722 3248.1.1.1 ↗ alpha complex topology › N-terminal domain in Lassa fever virus nucleoprotein › N-terminal domain in Lassa fever virus nucleoprotein › N-terminal domain in Lassa fever virus nucleoprotein › Arena_nucleocap 1.00 98.0 6.22e-01 100.0% 49.1%
3057624 3455.1.1.0 ↗ alpha arrays › WY-domain in RXLR effectors › WY-domain in RXLR effectors › WY-domain in RXLR effectors 0.65 40.0 4.02e-01 77.6% 59.1%
3525986 148.1.3.0 ↗ alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain 0.61 41.0 3.82e-01 70.6% 79.1%
3782436 616.1.1.0 ↗ alpha arrays › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain 0.58 42.0 4.36e-01 76.5% 87.5%
3707881 603.1.1.0 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.57 42.0 3.26e-01 76.5% 74.1%
5032064 604.3.1.0 ↗ alpha bundles › Spectrin repeat-like › BAG domain › BAG domain 0.57 40.0 4.11e-01 82.4% 78.5%
3225443 604.9.1.0 ↗ alpha bundles › Spectrin repeat-like › Ribosomal protein S20 › Ribosomal protein S20 0.56 42.0 3.82e-01 80.0% 58.3%
3929377 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.53 39.0 3.95e-01 80.0% 78.8%
3912386 150.3.1.1 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › 4-helical cytokines › 4-helical cytokine › Hormone_1 0.52 43.0 3.29e-01 90.6% 86.8%
D4 medium residues 191-255
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00843.23 best Arena_nucleocap 101.5 6.50e-29 100.0% 19.5%
CATH (10)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4fcyA01 1.10.10.60 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like 0.66 47.0 4.48e-01 96.9% 64.1%
4c23B02 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.59 45.0 3.14e-01 98.5% 23.5%
3jamD02 3.30.1140.32 Alpha Beta › 2-Layer Sandwich › Ribosomal protein S3 C-terminal domain › Ribosomal protein S3, C-terminal domain 0.58 47.0 3.77e-01 89.2% 66.9%
2b4lA02 3.10.105.10 Alpha Beta › Roll › Dipeptide-binding Protein; domain 3 › Dipeptide-binding Protein; Domain 3 0.57 46.0 3.55e-01 93.8% 86.0%
3lxzB02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.56 39.0 3.08e-01 73.8% 78.3%
1lfuP00 1.10.10.60 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like 0.55 46.0 4.33e-01 100.0% 75.6%
4p3gD00 1.10.3450.40 Mainly Alpha › Orthogonal Bundle › Hyaluronidase domain-like › Signal recognition particle, SRP68 subunit, RNA-binding domain 0.54 44.0 3.23e-01 95.4% 85.1%
5h20A00 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 0.52 45.0 3.95e-01 100.0% 80.6%
1zvzA02 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.52 42.0 3.45e-01 90.8% 91.1%
1wjtA00 1.20.930.10 Mainly Alpha › Up-down Bundle › Transcription Elongation Factor S-II; Chain A › Conserved domain common to transcription factors TFIIS, elongin A, CRSP70 0.51 37.0 3.15e-01 75.4% 69.9%
ECOD (8)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
406722 3248.1.1.1 ↗ alpha complex topology › N-terminal domain in Lassa fever virus nucleoprotein › N-terminal domain in Lassa fever virus nucleoprotein › N-terminal domain in Lassa fever virus nucleoprotein › Arena_nucleocap 0.95 90.0 5.52e-01 100.0% 20.2%
3707222 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.59 41.0 4.38e-01 93.8% 89.1%
4266983 304.48.1.32 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › TiaS-FLD 0.59 47.0 3.63e-01 100.0% 37.0%
3234593 3065.1.1.2 ↗ alpha bundles › Fatty acid- and retinoid-binding proteins › Fatty acid- and retinoid-binding proteins › Fatty acid- and retinoid-binding proteins › Gp-FAR-1 0.58 48.0 3.86e-01 100.0% 51.3%
3621947 196.1.1.1 ↗ alpha bundles › Regulator of G-protein signaling, RGS › Regulator of G-protein signaling, RGS › Regulator of G-protein signaling, RGS › RGS 0.57 45.0 3.99e-01 89.2% 88.0%
3708253 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.56 48.0 4.47e-01 100.0% 85.9%
3475805 108.1.1.140 ↗ alpha arrays › EF-hand › EF-hand-related › EF-hand › EF_EFCAB10_C 0.56 44.0 4.13e-01 89.2% 70.0%
3412191 632.1.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Families 57/38 glycoside transferase middle domain › Families 57/38 glycoside transferase middle domain 0.52 36.0 3.36e-01 72.3% 77.6%