1PDN | pdb_00001pdn

CRYSTAL STRUCTURE OF A PAIRED DOMAIN-DNA COMPLEX AT 2.5 ANGSTROMS RESOLUTION REVEALS STRUCTURAL BASIS FOR PAX DEVELOPMENTAL MUTATIONS

• PDB DOI: https://doi.org/10.2210/pdb1PDN/pdb
• NAKB: 1PDN

• Classification: GENE REGULATION/DNA
• Organism(s): Drosophila melanogaster
• Mutation(s): No 


• Deposited: 1995-05-16 Released: 1995-07-31 
• Deposition Author(s): Xu, W., Rould, M.A., Jun, S., Desplan, C., Pabo, C.O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.284 (Depositor) 
• R-Value Work: 
  0.234 (Depositor) 
• R-Value Observed: 
  0.234 (Depositor) 

Literature

Crystal structure of a paired domain-DNA complex at 2.5 A resolution reveals structural basis for Pax developmental mutations.

Xu, W., Rould, M.A., Jun, S., Desplan, C., Pabo, C.O.

(1995) Cell 80: 639-650

• PubMed: 7867071 
• DOI: https://doi.org/10.1016/0092-8674(95)90518-9
• Primary Citation Related Structures: 
  1PDN


• PubMed Abstract: 
  

  The 2.5 A resolution structure of a cocrystal containing the paired domain from the Drosophila paired (prd) protein and a 15 bp site shows structurally independent N-terminal and C-terminal subdomains. Each of these domains contains a helical region resembling the homeodomain and the Hin recombinase. The N-terminal domain makes extensive DNA contacts, using a novel beta turn motif that binds in the minor groove and a helix-turn-helix unit with a docking arrangement surprisingly similar to that of the lambda repressor. The C-terminal domain is not essential for prd binding and does not contact the optimized site. All known developmental missense mutations in the paired box of mammalian Pax genes map to the N-terminal subdomain, and most of them are found at the protein-DNA interface.

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Organizational Affiliation: 
• Department of Biology, Massachusetts Institute of Technology, Cambridge 02139.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 23.38 kDa 
• Atom Count: 1,534 
• Modeled Residue Count: 153 
• Deposited Residue Count: 158 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (PRD PAIRED)	C	128	Drosophila melanogaster	Mutation(s): 0  Gene Names: PRD
UniProt
Find proteins for P06601 (Drosophila melanogaster) Explore P06601  Go to UniProtKB:  P06601

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

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*TP*GP*TP*CP*AP*AP*CP*CP*GP*TP*GP*AP*CP*G)-3')	B	15	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.284 (Depositor) 
• R-Value Work:  0.234 (Depositor) 
• R-Value Observed: 0.234 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.6	α = 90
b = 68.6	β = 90
c = 100.5	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	refinement
DENZO	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 1995-07-31 
Deposition Author(s): Xu, W., Rould, M.A., Jun, S., Desplan, C., Pabo, C.O.

Revision History  

• Version 1.0: 1995-07-31
  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: 2024-02-14
  Changes: Data collection, Database references