1R9F Viral Protein Rna date Oct 28, 2003
title Crystal Structure Of P19 Complexed With 19-Bp Small Interfering Rna
authors K.Ye, L.Malinina, D.J.Patel
compound source
Molecule: 5'- R(Cpgpupapcpgpcpgpgpapapupapcpupupcpgpap Upu)-3';
Chain: B
Engineered: Yes
Synthetic: Yes
Other_details: 5'-Oh And 3'-Oh

Molecule: 5'- R(Upcpgpapapgpupapupupcpcpgpcpgpupapcpgp Upu)-3';
Chain: C
Engineered: Yes

Synthetic: Yes
Other_details: 5'-Oh And 3'-Oh

Molecule: Core Protein P19
Chain: A
Fragment: Residues 27-158
Engineered: Yes
Mutation: Yes

Organism_scientific: Tomato Bushy Stunt Virus
Organism_taxid: 12145
Gene: P19
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28a
symmetry Space Group: H 3 2
R_factor 0.212 R_Free 0.230
crystal
cell
length a length b length c angle alpha angle beta angle gamma
91.249 91.249 148.630 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.85 Å
ligand MSE, SO4 enzyme
note 1R9F (Molecule of the Month:pdb98)
related structures by homologous chain: 1RPU
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceRecognition of small interfering RNA by a viral suppressor of RNA silencing., Ye K, Malinina L, Patel DJ, Nature 2003 Dec 18;426(6968):874-8. Epub 2003 Dec 3. PMID:14661029
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (43 Kb) [Save to disk]
  • Biological Unit Coordinates (1r9f.pdb1.gz) 75 Kb
  • LPC: Ligand-Protein Contacts for 1R9F
  • CSU: Contacts of Structural Units for 1R9F
  • Likely Quarternary Molecular Structure file(s) for 1R9F
  • Structure Factors (344 Kb)
  • Retrieve 1R9F in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1R9F from S2C, [Save to disk]
  • Re-refined 1r9f structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1R9F in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 1R9F
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1R9F, from MSDmotif at EBI
  • Structure summary from SCOR (Structural Classification of RNA)
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1r9fa_, region A [Jmol] [rasmolscript] [script source]
  • Fold representative 1r9f from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1r9f] [1r9f_A] [1r9f_C] [1r9f_B]
  • SWISS-PROT database: [P11690]
  • Domain organization of [VP19_TBSVC] by SWISSPFAM
  • Other resources with information on 1R9F
  • Community annotation for 1R9F at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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