7XP3

DNA complex form of ORESARA1(ANAC092) NAC Domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.215 

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Literature

Structural basis of DNA binding by the NAC transcription factor ORE1, a master regulator of plant senescence.

Chun, I.Kim, H.J.Hong, S.Kim, Y.G.Kim, M.S.

(2023) Plant Commun 4: 100510-100510

  • DOI: https://doi.org/10.1016/j.xplc.2022.100510
  • Primary Citation of Related Structures:  
    7XLJ, 7XP3

  • PubMed Abstract: 

    Plants use sophisticated mechanisms of gene expression to control senescence in response to environmental stress or aging. ORE1 (Arabidopsis thaliana NAC092) is a master regulator of senescence that belongs to the plant-specific NAC transcription factor protein family. ORE1 has been reported to bind to multiple DNA targets to orchestrate leaf senescence, yet the mechanistic basis for recognition of the cognate gene sequence remains unclear. Here, we report the crystal structure of the ORE1-NAC domain alone and its DNA-binding form. The structure of DNA-bound ORE1-NAC revealed the molecular basis for nucleobase recognition and phosphate backbone interactions. We show that local versatility in the DNA-binding site, in combination with domain flexibility of the ORE-NAC homodimer, is crucial for the maintenance of binding to intrinsically flexible DNA. Our results provide a platform for understanding other plant-specific NAC protein-DNA interactions as well as insight into the structural basis of NAC regulators in plants of agronomic and scientific importance.


  • Organizational Affiliation

    Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk, Republic of Korea.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NAC domain-containing protein 92
A, B, C
159Arabidopsis thalianaMutation(s): 0 
Gene Names: NAC92NAC2NAC6ORE1At5g39610MIJ24.11
UniProt
Find proteins for Q9FKA0 (Arabidopsis thaliana)
Explore Q9FKA0 
Go to UniProtKB:  Q9FKA0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9FKA0
Sequence Annotations
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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*AP*GP*TP*TP*AP*CP*GP*TP*AP*CP*GP*GP*CP*AP*CP*AP*CP*GP*TP*AP*AP*C)-3')D [auth E]22DNA molecule
Sequence Annotations
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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(*TP*GP*TP*TP*AP*CP*GP*TP*GP*TP*GP*CP*CP*GP*TP*AP*CP*GP*TP*AP*AP*C)-3')E [auth F]22DNA molecule
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Entity ID: 4
MoleculeChains LengthOrganismImage
DNA (5'-D(P*GP*TP*TP*AP*CP*GP*TP*GP*TP*GP*C)-3')F [auth G]12DNA molecule
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Entity ID: 5
MoleculeChains LengthOrganismImage
DNA (5'-D(P*CP*AP*CP*AP*CP*GP*TP*AP*AP*C)-3')G [auth H]10DNA molecule
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.215 
  • Space Group: P 62
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.592α = 90
b = 92.592β = 90
c = 216.9γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data collection
PHENIXphasing
HKL-2000data reduction

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Korea)Korea, Republic Of--

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-29
    Type: Initial release
  • Version 1.1: 2023-05-24
    Changes: Database references