Biological Assembly 1  

 3D View: Structure | Electron Density | Validation Report

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 47.72 kDa 
• Atom Count: 3292 
• Modelled Residue Count: 318 
• Deposited Residue Count: 368 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

1MNN

Structure of the sporulation specific transcription factor Ndt80 bound to DNA

• DOI: 10.2210/pdb1MNN/pdb
• NDB: PD0341

• Classification: TRANSCRIPTION/DNA
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2002-09-05 Released: 2002-11-20 
• Deposition Author(s): Lamoureux, J.S., Stuart, D., Tsang, R., Wu, C., Glover, J.N.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.206 
• R-Value Work: 0.195 
• R-Value Observed: 0.195 

Literature

Structure of the sporulation-specific transcription factor Ndt80 bound to DNA

Lamoureux, J.S., Stuart, D., Tsang, R., Wu, C., Glover, J.N.

(2002) EMBO J 21: 5721-5732

• PubMed: 12411490 
• DOI: 10.1093/emboj/cdf572
• Primary Citation of Related Structures:  
  1MN4, 1MNN


• PubMed Abstract: 
  

Progression through the middle phase of sporulation in Saccharomyces cerevisiae is promoted by the successful completion of recombination at the end of prophase I. Completion of meiotic recombination allows the activation of the sporulation-specific transcription factor Ndt80, which binds to a specific DNA sequence, the middle sporulation element (MSE), and activates approximately 150 genes to enable progression through meiosis. Here, we isolate the DNA-binding domain of Ndt80 and determine its crystal structure both free and in complex with an MSE-containing DNA. The structure reveals that Ndt80 is a member of the Ig-fold family of transcription factors. The structure of the DNA-bound form, refined at 1.4 A, reveals an unexpected mode of recognition of 5'-pyrimidine- guanine-3' dinucleotide steps by arginine residues that simultaneously recognize the 3'-guanine base through hydrogen bond interactions and the 5'-pyrimidine through stacking/van der Waals interactions. Analysis of the DNA-binding affinities of MSE mutants demonstrates the central importance of these interactions, and of the AT-rich portion of the MSE. Functional similarities between Ndt80 and the Caenorhabditis elegans p53 homolog suggest an evolutionary link between Ndt80 and the p53 family.

---

Organizational Affiliation: 

Department of Biochemistry, University of Alberta, Edmonton, AB, T6G 2H7, Canada.

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
NDT80 protein	C [auth A]	340	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: NDT80
UniProt
Find proteins for P38830 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38830  Go to UniProtKB:  P38830

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*TP*GP*CP*GP*AP*CP*AP*CP*AP*AP*AP*AP*AP*C)-3'	A [auth B]	14	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*AP*GP*TP*TP*TP*TP*TP*GP*TP*GP*TP*CP*GP*C)-3'	B [auth C]	14	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.206 
• R-Value Work: 0.195 
• R-Value Observed: 0.195 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.143	α = 90
b = 78.887	β = 90
c = 161.522	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-09-05 
• Released Date: 2002-11-20 
Deposition Author(s): Lamoureux, J.S., Stuart, D., Tsang, R., Wu, C., Glover, J.N.

Revision History  

• Version 1.0: 2002-11-20
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance