4PRF Rna Binding Protein Rna date Mar 05, 2014
title A Second Look At The Hdv Ribozyme Structure And Dynamics.
authors G.J.Kapral, S.Jain, J.Noeske, J.A.Doudna, D.C.Richardson, J.S.Ric
compound source
Molecule: Hepatitis Delta Virus Ribozyme
Chain: B
Engineered: Yes
Synthetic: Yes
Other_details: Rna Occurs From Hapatitis Delta Virus Pathog Vitro Transcription With Puc19;

Molecule: U1 Small Nuclear Ribonucleoprotein A
Chain: A
Fragment: U1a_rbd, Unp Residues 98-173
Synonym: U1 Snrnp A, U1-A, U1a
Engineered: Yes
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Snrpa
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet
symmetry Space Group: H 3 2
R_factor 0.198 R_Free 0.252
crystal
cell
length a length b length c angle alpha angle beta angle gamma
108.944 108.944 191.754 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.40 Å
ligand SR enzyme
note 4PRF supersedes 1VC7
Primary referenceNew tools provide a second look at HDV ribozyme structure, dynamics and cleavage., Kapral GJ, Jain S, Noeske J, Doudna JA, Richardson DC, Richardson JS, Nucleic Acids Res. 2014 Oct 17. pii: gku992. PMID:25326328
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (138 Kb) [Save to disk]
  • Biological Unit Coordinates (4prf.pdb1.gz) 133 Kb
  • LPC: Ligand-Protein Contacts for 4PRF
  • CSU: Contacts of Structural Units for 4PRF
  • Structure Factors (136 Kb)
  • Retrieve 4PRF in mmCIF format [Save to disk]
  • Re-refined 4prf structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4PRF 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 4PRF
  • 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 4PRF, from MSDmotif at EBI
  • Fold representative 4prf from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4prf_B] [4prf] [4prf_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4PRF
  • Community annotation for 4PRF at PDBWiki (http://pdbwiki.org)

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