1L8R

Structure of the Retinal Determination Protein Dachshund Reveals a DNA-Binding Motif

• PDB DOI: https://doi.org/10.2210/pdb1L8R/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2002-03-21 Released: 2002-06-26 
• Deposition Author(s): Kim, S.S., Zhang, R., Braunstein, S.E., Joachimiak, A., Cvekl, A., Hegde, R.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.259 
• R-Value Work: 0.237 
• R-Value Observed: 0.237 

Literature

Structure of the retinal determination protein Dachshund reveals a DNA binding motif.

Kim, S.S., Zhang, R.G., Braunstein, S.E., Joachimiak, A., Cvekl, A., Hegde, R.S.

(2002) Structure 10: 787-795

• PubMed: 12057194 
• DOI: https://doi.org/10.1016/s0969-2126(02)00769-4
• Primary Citation of Related Structures:  
  1L8R


• PubMed Abstract: 
  

  The Dachshund proteins are essential components of a regulatory network controlling cell fate determination. They have been implicated in eye, limb, brain, and muscle development. These proteins cannot be assigned to any recognizable structural or functional class based on amino acid sequence analysis. The 1.65 A crystal structure of the most conserved domain of human DACHSHUND is reported here. The protein forms an alpha/beta structure containing a DNA binding motif similar to that found in the winged helix/forkhead subgroup of the helix-turn-helix family. This unexpected finding alters the previously proposed molecular models for the role of Dachshund in the eye determination pathway. Furthermore, it provides a rational framework for future mechanistic analyses of the Dachshund proteins in several developmental contexts.

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Organizational Affiliation: 

Structural Biology Program, Skirball Institute, New York University Medical Center, New York, NY 10016, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 22.57 kDa 
• Atom Count: 1,692 
• Modelled Residue Count: 200 
• Deposited Residue Count: 202 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dachshund	A, B	101	Homo sapiens	Mutation(s): 1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UI36 (Homo sapiens) Explore Q9UI36  Go to UniProtKB:  Q9UI36
PHAROS:  Q9UI36 GTEx:  ENSG00000276644

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.259 
• R-Value Work: 0.237 
• R-Value Observed: 0.237 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 28.797	α = 60.75
b = 47.731	β = 86.86
c = 50.436	γ = 84.55

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-06-26 
Deposition Author(s): Kim, S.S., Zhang, R., Braunstein, S.E., Joachimiak, A., Cvekl, A., Hegde, R.S.

Revision History  

• Version 1.0: 2002-06-26
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary