1HDD

CRYSTAL STRUCTURE OF AN ENGRAILED HOMEODOMAIN-DNA COMPLEX AT 2.8 ANGSTROMS RESOLUTION: A FRAMEWORK FOR UNDERSTANDING HOMEODOMAIN-DNA INTERACTIONS

• PDB DOI: https://doi.org/10.2210/pdb1HDD/pdb
• NAKB: 1HDD

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


• Deposited: 1991-09-16 Released: 1992-01-15 
• Deposition Author(s): Kissinger, C.R., Liu, B., Martin-Blanco, E., Kornberg, T.B., Pabo, C.O.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Work: 0.225 
• R-Value Observed: 0.225 

Literature

Crystal structure of an engrailed homeodomain-DNA complex at 2.8 A resolution: a framework for understanding homeodomain-DNA interactions.

Kissinger, C.R., Liu, B.S., Martin-Blanco, E., Kornberg, T.B., Pabo, C.O.

(1990) Cell 63: 579-590

• PubMed: 1977522 
• DOI: https://doi.org/10.1016/0092-8674(90)90453-l
• Primary Citation of Related Structures:  
  1HDD


• PubMed Abstract: 
  

  The crystal structure of a complex containing the engrailed homeodomain and a duplex DNA site has been determined at 2.8 A resolution and refined to a crystallographic R factor of 24.4%. In this complex, two separate regions of the 61 amino acid polypeptide contact a TAAT subsite. An N-terminal arm fits into the minor groove, and the side chains of Arg-3 and Arg-5 make contacts near the 5' end of this "core consensus" binding site. An alpha helix fits into the major groove, and the side chains of IIe-47 and Asn-51 contact base pairs near the 3' end of the TAAT site. This "recognition helix" is part of a structurally conserved helix-turn-helix unit, but these helices are longer than the corresponding helices in the lambda repressor, and the relationship between the helix-turn-helix unit and the DNA is significantly different.

---

Organizational Affiliation: 

Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 27.82 kDa 
• Atom Count: 1,817 
• Modelled Residue Count: 156 
• Deposited Residue Count: 164 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (ENGRAILED HOMEODOMAIN)	C, D	61	Drosophila melanogaster	Mutation(s): 0
UniProt
Find proteins for P02836 (Drosophila melanogaster) Explore P02836  Go to UniProtKB:  P02836

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*TP*TP*TP*GP*CP*CP*AP*TP*GP*TP*AP*AP*TP*TP*AP*C P*CP*TP*AP*A)-3')	A	21	synthetic construct

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*TP*TP*AP*GP*GP*TP*AP*AP*TP*TP*AP*CP*AP*TP*GP*G P*CP*AP*AP*A)-3')	B	21	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Work: 0.225 
• R-Value Observed: 0.225 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 131.2	α = 90
b = 45.5	β = 119
c = 72.9	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1992-01-15 
Deposition Author(s): Kissinger, C.R., Liu, B., Martin-Blanco, E., Kornberg, T.B., Pabo, C.O.

Revision History  

• Version 1.0: 1992-01-15
  Type: Initial release
  
• Version 1.1: 2008-05-22
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-02-15
  Changes: Source and taxonomy, Structure summary
• Version 1.4: 2022-12-21
  Changes: Database references