1JGG | pdb_00001jgg

Even-skipped Homeodomain Complexed to AT-rich DNA

• PDB DOI: https://doi.org/10.2210/pdb1JGG/pdb
• NAKB: 1JGG

• Classification: TRANSCRIPTION/DNA
• Organism(s): Drosophila melanogaster
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2001-06-25 Released: 2001-07-06 
• Deposition Author(s): Hirsch, J.A., Aggarwal, A.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.316 (Depositor) 
• R-Value Work: 
  0.229 (Depositor) 

Literature

Structure of the even-skipped homeodomain complexed to AT-rich DNA: new perspectives on homeodomain specificity.

Hirsch, J.A., Aggarwal, A.K.

(1995) EMBO J 14: 6280-6291

• PubMed: 8557047 
• DOI: https://doi.org/10.1002/j.1460-2075.1995.tb00318.x
• Primary Citation Related Structures: 
  1JGG


• PubMed Abstract: 
  

  even-skipped is a homeobox gene important in controlling segment patterning in the embryonic fruit fly. Its homeobox encodes a DNA binding domain which binds with similar affinities to two DNA consensus sequences, one AT-rich, the other GC-rich. We describe a crystallographic analysis of the Even-skipped homeodomain complexed to an AT-rich oligonucleotide at 2.0 A resolution. The structure reveals a novel arrangement of two homeodomains bound to one 10 bp DNA sequence in a tandem fashion. This arrangement suggests a mechanism for the homeoproteins' regulatory specificity. In addition, the functionally important residue Gln50 is observed in multiple conformations making direct and water-mediated hydrogen bonds with the DNA bases.

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Organizational Affiliation: 
• Department of Biochemistry and Molecular Biophysics, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 21.19 kDa 
• Atom Count: 1,541 
• Modeled Residue Count: 134 
• Deposited Residue Count: 140 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Segmentation Protein Even-Skipped	C [auth A], D [auth B]	60	Drosophila melanogaster	Mutation(s): 0
UniProt
Find proteins for P06602 (Drosophila melanogaster) Explore P06602  Go to UniProtKB:  P06602

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(P*TP*AP*AP*TP*TP*GP*AP*AP*TP*T)-3'	A [auth C]	10	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(P*AP*AP*TP*TP*CP*AP*AP*TP*TP*A)-3'	B [auth D]	10	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.316 (Depositor) 
• R-Value Work:  0.229 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.06	α = 90
b = 61.61	β = 90
c = 39.99	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
CCP4	data scaling
ROTAVATA	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-07-06 
Deposition Author(s): Hirsch, J.A., Aggarwal, A.K.

Revision History  

• Version 1.0: 2001-07-06
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-04
  Changes: Refinement description
• Version 1.4: 2024-02-07
  Changes: Data collection, Database references