5E3H Hydrolase Rna date Oct 02, 2015
title Structural Basis For Rna Recognition And Activation Of Rig-I
authors F.Jiang, M.T.Miller, J.Marcotrigiano
compound source
Molecule: Probable Atp-Dependent Rna Helicase Ddx58
Chain: A
Fragment: Unp Residues 232-925
Synonym: Dead Box Protein 58,Rig-I-Like Receptor 1,Rlr-1,Re Acid-Inducible Gene 1 Protein,Rig-1,Retinoic Acid-Inducible Protein,Rig-I;
Ec: 3.6.4.13
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ddx58
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Rosetta(De3)
Expression_system_vector_type: Modified Pet 28a
Expression_system_plasmid: Rig-I (232-925), Rig-I Deltacard

Molecule: Rna (5'-R(Cpgpapcpgpcpupapgpcpgpu)-3'
Chain: B, C
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 65 2 2
R_factor 0.234 R_Free 0.268
crystal
cell
length a length b length c angle alpha angle beta angle gamma
176.030 176.030 108.071 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.70 Å
ligand ADP, BEF, GOL, MG, ZN enzyme Hydrolase E.C.3.6.4.13 BRENDA
note 5E3H supersedes 3TMI
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructural basis of RNA recognition and activation by innate immune receptor RIG-I., Jiang F, Ramanathan A, Miller MT, Tang GQ, Gale M, Patel SS, Marcotrigiano J, Nature. 2011 Sep 25. doi: 10.1038/nature10537. PMID:21947008
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (239 Kb) [Save to disk]
  • Biological Unit Coordinates (5e3h.pdb1.gz) 232 Kb
  • LPC: Ligand-Protein Contacts for 5E3H
  • CSU: Contacts of Structural Units for 5E3H
  • Structure Factors (771 Kb)
  • Retrieve 5E3H in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5E3H from S2C, [Save to disk]
  • Re-refined 5e3h structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5E3H 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 5E3H
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5e3h] [5e3h_A] [5e3h_B] [5e3h_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 5E3H: [AAA] [DEXDc] [HELICc ] by SMART
  • Other resources with information on 5E3H
  • Community annotation for 5E3H at PDBWiki (http://pdbwiki.org)

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