› 5ip2

X-ray diffraction
3.3Å resolution

Tomato spotted wilt tospovirus nucleocapsid protein-ssRNA complex

Released:
DOI: 10.2210/pdb5ip2/pdb
PDB entry 5ip2 coloured by chain, front view.
PDB entry 5ip2 coloured by chain, side view.
PDB entry 5ip2 coloured by chain, top view.
Source organisms:
Primary publication:
Asymmetric Trimeric Ring Structure of the Nucleocapsid Protein of Tospovirus.
Komoda K, Narita M, Yamashita K, Tanaka I, Yao M
J Virol 91 (2017)
PMID: 28768868

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:
Sequence domain:

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-514492 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct RNA molecules
Macromolecules (3 distinct):
Nucleoprotein Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 279 amino acids
Theoretical weight: 31.5 KDa
Source organism: Orthotospovirus tomatomaculae
Expression system: Escherichia coli
UniProt:
  • Canonical: F4ZD19 (Residues: 1-258; Coverage: 100%)
Gene name: N
Sequence domains: Tospovirus nucleocapsid protein
RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3') Chain: E
Molecule details ›
Chain: E
Length: 19 nucleotides
Theoretical weight: 5.77 KDa
Source organism: synthetic construct
Expression system: Not provided
RNA (5'-D(P*UP*UP*U)-3') Chains: D, F
Molecule details ›
Chains: D, F
Length: 3 nucleotides
Theoretical weight: 874 Da
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-17A
Spacegroup: P21
Unit cell:
a: 68.208Å b: 94.732Å c: 70.917Å
α: 90° β: 112.6° γ: 90°
R-values:
R R work R free
0.285 0.282 0.317
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

8 review citations

The RNA-Dependent RNA Polymerase NIb of Potyviruses Plays Multifunctional, Contrasting Roles during Viral Infection.
Shen et al. (2020)
7 more

3 mentions without citation

Potyvirus virion structure shows conserved protein fold and RNA binding site in ssRNA viruses.
Zamora et al. (2017)
2 more