3AAF Dna Binding Protein Dna date Nov 16, 2009
title Structure Of Wrn Rqc Domain Bound To Double-Stranded Dna
authors K.Kitano, T.Hakoshima
compound source
Molecule: Werner Syndrome Atp-Dependent Helicase
Chain: A, B
Fragment: Recq C-Terminal (Rqc) Domain
Synonym: Werner Syndrome Protein, Wrn
Ec: 3.6.1.-
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21-Codonplus Ril
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgex-5x-1

Molecule: Dna (5'-D(Apcpcpcptpapaptptpapgpgpgp
Chain: C, D
Engineered: Yes

Synthetic: Yes
symmetry Space Group: P 43 2 2
R_factor 0.212 R_Free 0.244
length a length b length c angle alpha angle beta angle gamma
84.077 84.077 145.291 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.90 Å
ligand ACT enzyme Hydrolase E.C.3.6.1 BRENDA
A, B

Primary referenceStructural basis for DNA strand separation by the unconventional winged-helix domain of RecQ helicase WRN., Kitano K, Kim SY, Hakoshima T, Structure. 2010 Feb 10;18(2):177-87. PMID:20159463
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (60 Kb) [Save to disk]
  • Biological Unit Coordinates (3aaf.pdb1.gz) 54 Kb
  • LPC: Ligand-Protein Contacts for 3AAF
  • CSU: Contacts of Structural Units for 3AAF
  • Structure Factors (299 Kb)
  • Retrieve 3AAF in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3AAF from S2C, [Save to disk]
  • Re-refined 3aaf structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3AAF 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 3AAF
  • 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 3AAF, from MSDmotif at EBI
  • Fold representative 3aaf from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3aaf_B] [3aaf_C] [3aaf_D] [3aaf_A] [3aaf]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3AAF: [RQC ] by SMART
  • Alignments of the sequence of 3AAF with the sequences similar proteins can be viewed for 3AAF's classification at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification at ProtoMap. Click on the Cluster number.
  • Other resources with information on 3AAF
  • Community annotation for 3AAF 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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