4N41 Nuclear Protein Dna date Oct 08, 2013
title Structure Of Thermus Thermophilus Argonaute Bound To Guide D Mer Target Dna
authors G.Sheng, H.Zhao, J.Wang, Y.Rao, Y.Wang
compound source
Molecule: Argonaute
Chain: A, B
Engineered: Yes
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274
Strain: Thermophilus
Gene: Argonaute, Tt_p0026
Expression_system: Escherichia Coli
Expression_system_taxid: 511693
Expression_system_strain: Rosetta
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-Sumo

Molecule: 5'-D(Ptpgpapgpgptpapgptpapgpgptptg Apgpt)-3';
Chain: C, E
Engineered: Yes

Synthetic: Yes

Molecule: 5'-D(Papcpcptpapcptpapcpcptpcpg)-3'
Chain: D
Engineered: Yes

Synthetic: Yes

Molecule: 5'-D(Apapcpcptpapcptpgpcpcptpcpg)-3
Chain: F
Engineered: Yes

Synthetic: Yes
symmetry Space Group: P 1 21 1
R_factor 0.223 R_Free 0.259
length a length b length c angle alpha angle beta angle gamma
59.513 101.699 153.019 90.00 93.52 90.00
method X-Ray Diffractionresolution 2.25 Å
ligand MG enzyme
Gene TT
A, B

Primary referenceStructure-based cleavage mechanism of Thermus thermophilus Argonaute DNA guide strand-mediated DNA target cleavage., Sheng G, Zhao H, Wang J, Rao Y, Tian W, Swarts DC, van der Oost J, Patel DJ, Wang Y, Proc Natl Acad Sci U S A. 2013 Dec 27. PMID:24374628
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (237 Kb) [Save to disk]
  • Biological Unit Coordinates (4n41.pdb1.gz) 117 Kb
  • Biological Unit Coordinates (4n41.pdb2.gz) 117 Kb
  • LPC: Ligand-Protein Contacts for 4N41
  • CSU: Contacts of Structural Units for 4N41
  • Structure Factors (1793 Kb)
  • Retrieve 4N41 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4N41 from S2C, [Save to disk]
  • Re-refined 4n41 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4N41 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 4N41
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4N41, from MSDmotif at EBI
  • Fold representative 4n41 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4n41_D] [4n41_F] [4n41] [4n41_A] [4n41_B] [4n41_E] [4n41_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4N41: [Piwi ] by SMART
  • Other resources with information on 4N41
  • Community annotation for 4N41 at PDBWiki (http://pdbwiki.org)

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