2EVH | pdb_00002evh

Structure of a Ndt80-DNA complex (MSE mutant mA7G)

• PDB DOI: https://doi.org/10.2210/pdb2EVH/pdb
• NAKB: 2EVH

• Classification: CELL CYCLE/DNA
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2005-10-31 Released: 2006-03-21 
• Deposition Author(s): Lamoureux, J.S., Glover, J.N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free: 
  0.212 (Depositor), 0.232 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.212 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Starting Model: experimental

Literature

Principles of Protein-DNA Recognition Revealed in the Structural Analysis of Ndt80-MSE DNA Complexes.

Lamoureux, J.S., Glover, J.N.

(2006) Structure 14: 555-565

• PubMed: 16531239 
• DOI: https://doi.org/10.1016/j.str.2005.11.017
• Primary Citation Related Structures: 
  2ETW, 2EUV, 2EUW, 2EUX, 2EUZ, 2EVF, 2EVG, 2EVH, 2EVI, 2EVJ


• PubMed Abstract: 
  

  The Saccharomyces cerevisiae transcription factor Ndt80 selectively binds a DNA consensus sequence (the middle sporulation element [MSE]) to activate gene expression after the successful completion of meiotic recombination. Here we report the X-ray crystal structures of Ndt80 bound to ten distinct MSE variants. Comparison of these structures with the structure of Ndt80 bound to a consensus MSE reveals structural principles that determine the DNA binding specificity of this transcription factor. The 5' GC-rich end of the MSE contains distinct 5'-YpG-3' steps that are recognized by arginine side chains through a combination of hydrogen bonding and cation-pi interactions. The 3' AT-rich region is recognized via minor groove contacts that sterically exclude the N2 atom of GC base pairs. The conformation of the AT-rich region is fixed by interactions with the protein that favor recognition of poly(A)-poly(T) versus mixed AT sequences through an avoidance of major groove steric clashes at 5'-ApT-3' steps.

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Organizational Affiliation: 
• Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 48.15 kDa 
• Atom Count: 3,252 
• Modeled Residue Count: 317 
• Deposited Residue Count: 373 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
NDT80 protein	C [auth A]	345	Saccharomyces cerevisiae	Mutation(s): 2  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*GP*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*CP*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: 1.99 Å
• R-Value Free:  0.212 (Depositor), 0.232 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.212 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.534	α = 90
b = 78.441	β = 90
c = 161.334	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-03-21 
Deposition Author(s): Lamoureux, J.S., Glover, J.N.

Revision History  

• Version 1.0: 2006-03-21
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2021-10-20
  Changes: Database references
• Version 1.5: 2023-08-23
  Changes: Data collection, Refinement description