3HVR Nucleic Acid Binding Protein Dna Rna date Jun 16, 2009
title Crystal Structure Of T. Thermophilus Argonaute Complexed Wit Guide Strand And 19-Nt Rna Target Strand With Two Mg2+ At T Cleavage Site
authors Y.Wang, H.Li, G.Sheng, D.J.Patel
compound source
Molecule: Argonaute
Chain: A, B
Engineered: Yes
Organism_scientific: Thermus Thermophilus
Organism_taxid: 262724
Strain: Hb27
Gene: Tt_p0026
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Rosetta 2 (De3)Plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-Sumo

Molecule: 5'-D(Ptpgpapgpgptpapgptpapgpgptptp Papgpt)-3';
Chain: C, M
Engineered: Yes

Synthetic: Yes

Molecule: 5'-R(Upapupapcpapapcpcpupapcpupapc G)-3';
Chain: D, N
Engineered: Yes

Synthetic: Yes
symmetry Space Group: P 21 21 21
R_factor 0.226 R_Free 0.273
crystal
cell
length a length b length c angle alpha angle beta angle gamma
111.252 116.903 170.504 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.21 Å
ligand MG, PO4 enzyme
Gene TT
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceNucleation, propagation and cleavage of target RNAs in Ago silencing complexes., Wang Y, Juranek S, Li H, Sheng G, Wardle GS, Tuschl T, Patel DJ, Nature. 2009 Oct 8;461(7265):754-61. PMID:19812667
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (220 Kb) [Save to disk]
  • Biological Unit Coordinates (3hvr.pdb1.gz) 108 Kb
  • Biological Unit Coordinates (3hvr.pdb2.gz) 108 Kb
  • LPC: Ligand-Protein Contacts for 3HVR
  • CSU: Contacts of Structural Units for 3HVR
  • Structure Factors (482 Kb)
  • Retrieve 3HVR in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3HVR from S2C, [Save to disk]
  • Re-refined 3hvr structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3HVR 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 3HVR
  • 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
  • 3D motif for 3HVR, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3hvr_C] [3hvr_B] [3hvr] [3hvr_D] [3hvr_N] [3hvr_M] [3hvr_A]
  • SWISS-PROT database: [Q746M7]
  • Domain organization of [Q746M7_THET2] by SWISSPFAM
  • Domain found in 3HVR: [Piwi ] by SMART
  • Other resources with information on 3HVR
  • Community annotation for 3HVR 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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