3DLH Nucleic Acid Binding Protein Dna date Jun 27, 2008
title Crystal Structure Of The Guide-Strand-Containing Argonaute Protein Silencing Complex
authors Y.Wang, 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: Dna (5'- D(Dtpdgpdapdgpdgpdtpdapdgpdtpdapdgpdgpdtpdtpd Gpdtpdapdtpdapdgpdt)-3');
Chain: X, Y
Engineered: Yes

Synthetic: Yes
symmetry Space Group: P 21 21 21
R_factor 0.226 R_Free 0.284
length a length b length c angle alpha angle beta angle gamma
74.744 114.629 175.689 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.00 Å
ligand ACY, MG, PGE, PO4 enzyme
Gene TT
A, B

Primary referenceStructure of the guide-strand-containing argonaute silencing complex., Wang Y, Sheng G, Juranek S, Tuschl T, Patel DJ, Nature. 2008 Aug 27. PMID:18754009
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (231 Kb) [Save to disk]
  • Biological Unit Coordinates (3dlh.pdb1.gz) 115 Kb
  • Biological Unit Coordinates (3dlh.pdb2.gz) 111 Kb
  • LPC: Ligand-Protein Contacts for 3DLH
  • CSU: Contacts of Structural Units for 3DLH
  • Likely Quarternary Molecular Structure file(s) for 3DLH
  • Structure Factors (372 Kb)
  • Retrieve 3DLH in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3DLH from S2C, [Save to disk]
  • Re-refined 3dlh structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3DLH 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 3DLH
  • 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 3DLH, from MSDmotif at EBI
  • Fold representative 3dlh from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3dlh_B] [3dlh_X] [3dlh_Y] [3dlh] [3dlh_A]
  • SWISS-PROT database: [Q746M7]
  • Domain organization of [Q746M7_THET2] by SWISSPFAM
  • Domain found in 3DLH: [Piwi ] by SMART
  • Other resources with information on 3DLH
  • Community annotation for 3DLH 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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