1J75

Crystal Structure of the DNA-Binding Domain Zalpha of DLM-1 Bound to Z-DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of the DLM-1-Z-DNA complex reveals a conserved family of Z-DNA-binding proteins.

Schwartz, T.Behlke, J.Lowenhaupt, K.Heinemann, U.Rich, A.

(2001) Nat.Struct.Mol.Biol. 8: 761-765

  • DOI: 10.1038/nsb0901-761
  • Also Cited By: 1XMK

  • PubMed Abstract: 
  • The first crystal structure of a protein, the Z alpha high affinity binding domain of the RNA editing enzyme ADAR1, bound to left-handed Z-DNA was recently described. The essential set of residues determined from this structure to be critical for Z-D ...

    The first crystal structure of a protein, the Z alpha high affinity binding domain of the RNA editing enzyme ADAR1, bound to left-handed Z-DNA was recently described. The essential set of residues determined from this structure to be critical for Z-DNA recognition was used to search the database for other proteins with the potential for Z-DNA binding. We found that the tumor-associated protein DLM-1 contains a domain with remarkable sequence similarities to Z alpha(ADAR). Here we report the crystal structure of this DLM-1 domain bound to left-handed Z-DNA at 1.85 A resolution. Comparison of Z-DNA binding by DLM-1 and ADAR1 reveals a common structure-specific recognition core within the binding domain. However, the domains differ in certain residues peripheral to the protein-DNA interface. These structures reveal a general mechanism of Z-DNA recognition, suggesting the existence of a family of winged-helix proteins sharing a common Z-DNA binding motif.


    Organizational Affiliation

    Max-Delbrück-Centrum für Molekulare Medizin, Robert-Rössle-Str. 10, D-13125 Berlin, Germany. Thomas.Schwartz@mail.rockefeller.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Tumor Stroma and Activated Macrophage Protein DLM-1
A
67Mus musculusGene Names: Zbp1 (Dlm1)
Find proteins for Q9QY24 (Mus musculus)
Go to UniProtKB:  Q9QY24
Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*TP*CP*GP*CP*GP*CP*G)-3'B7N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.218 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 63.611α = 90.00
b = 63.611β = 90.00
c = 72.238γ = 120.00
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-09-01
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2011-11-16
    Type: Atomic model