9ANT | pdb_00009ant

ANTENNAPEDIA HOMEODOMAIN-DNA COMPLEX

• PDB DOI: https://doi.org/10.2210/pdb9ANT/pdb
• NAKB: 9ANT

• Classification: TRANSCRIPTION/DNA
• Organism(s): Drosophila melanogaster
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 1998-07-02 Released: 1998-10-14 
• Deposition Author(s): Fraenkel, E., Pabo, C.O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.239 (Depositor) 
• R-Value Work: 
  0.218 (Depositor) 
• R-Value Observed: 
  0.218 (Depositor) 

Literature

Comparison of X-ray and NMR structures for the Antennapedia homeodomain-DNA complex.

Fraenkel, E., Pabo, C.O.

(1998) Nat Struct Biol 5: 692-697

• PubMed: 9699632 
• DOI: https://doi.org/10.1038/1382
• Primary Citation Related Structures: 
  9ANT


• PubMed Abstract: 
  

  Homeodomains are one of the key families of eukaryotic DNA-binding motifs and provide an important model system for studying protein-DNA interactions. We have crystallized the Antennapedia homeodomain-DNA complex and solved this structure at 2.4 A resolution. NMR and molecular dynamics studies had implied that this homeodomain achieves specificity through an ensemble of rapidly fluctuating DNA contacts. The crystal structure is in agreement with the underlying NMR data, but our structure reveals a well-defined set of contacts and also reveals the locations and roles of water molecules at the protein-DNA interface. The synthesis of X-ray and NMR studies provides a unified, general model for homeodomain-DNA interactions.

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Organizational Affiliation: 
• Department of Biology, Massachusetts Institute of Technology, Cambridge 02139, 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: 34.59 kDa 
• Atom Count: 2,297 
• Modeled Residue Count: 172 
• Deposited Residue Count: 184 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ANTENNAPEDIA HOMEODOMAIN	E [auth A], F [auth B]	62	Drosophila melanogaster	Mutation(s): 1
UniProt
Find proteins for P02833 (Drosophila melanogaster) Explore P02833  Go to UniProtKB:  P02833

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*GP*AP*AP*AP*GP*CP*CP*AP*TP*TP*AP*GP*AP*G)-3')	A [auth C], C [auth E]	15	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*CP*TP*CP*TP*AP*AP*TP*GP*GP*CP*TP*TP*TP*C)-3')	B [auth D], D [auth F]	15	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NI	G [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.239 (Depositor) 
• R-Value Work:  0.218 (Depositor) 
• R-Value Observed: 0.218 (Depositor) 

Space Group: P 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.05	α = 90
b = 77.75	β = 90
c = 94.42	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-10-14 
Deposition Author(s): Fraenkel, E., Pabo, C.O.

Revision History  

• Version 1.0: 1998-10-14
  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: 2021-11-03
  Changes: Database references, Derived calculations
• Version 1.4: 2024-02-14
  Changes: Data collection