1F8V Virus Rna date Jul 05, 2000
title The Structure Of Pariacoto Virus Reveals A Dodecahedral Cage Rna
authors L.Tang, K.N.Johnson, L.A.Ball, T.Lin, M.Yeager, J.E.Johnson
compound source
Molecule: Rna
Chain: R
Organism_scientific: Pariacato Virus
Organism_taxid: 103782

Molecule: Mature Capsid Protein Beta
Chain: A, B, C

Organism_scientific: Pariacato Virus
Organism_taxid: 103782

Molecule: Mature Capsid Protein Gamma
Chain: D, E, F

Organism_scientific: Pariacato Virus
Organism_taxid: 103782
symmetry Space Group: P 1 21 1
R_factor 0.219 R_Free 0.221
crystal
cell
length a length b length c angle alpha angle beta angle gamma
329.332 346.944 424.893 90.00 90.83 90.00
method X-Ray Diffractionresolution 3.00 Å
ligand CA, SO4 enzyme
note 1F8V is a representative structure
Gene
Ontology
ChainFunctionProcessComponent
A, C, B


Primary referenceThe structure of pariacoto virus reveals a dodecahedral cage of duplex RNA., Tang L, Johnson KN, Ball LA, Lin T, Yeager M, Johnson JE, Nat Struct Biol 2001 Jan;8(1):77-83. PMID:11135676
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (188 Kb) [Save to disk]
  • Biological Unit Coordinates (1f8v.pdb1.gz) 10153 Kb
  • LPC: Ligand-Protein Contacts for 1F8V
  • CSU: Contacts of Structural Units for 1F8V
  • Likely Quarternary Molecular Structure file(s) for 1F8V
  • Structure Factors (13741 Kb)
  • Retrieve 1F8V in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1F8V from S2C, [Save to disk]
  • Re-refined 1f8v structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1F8V 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 1F8V
  • VIPERdb: visual, structural and computational analysis of 1F8V
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1F8V, from MSDmotif at EBI
  • Structure summary from SCOR (Structural Classification of RNA)
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1f8v.1, region A:,D [Jmol] [rasmolscript] [script source]
        - Domain d1f8v.2, region B:,E [Jmol] [rasmolscript] [script source]
        - Domain d1f8v.3, region C:,F [Jmol] [rasmolscript] [script source]
  • Fold representative 1f8v from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1f8v_C] [1f8v_E] [1f8v_B] [1f8v_A] [1f8v_F] [1f8v] [1f8v_R] [1f8v_D]
  • SWISS-PROT database: [Q9J7Z0]
  • Domain organization of [COAT_PAV] by SWISSPFAM
  • Other resources with information on 1F8V
  • Community annotation for 1F8V 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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