7WQ5 | pdb_00007wq5

Crystal structure of Arabidopsis transcriptional factor WRINKLED1 with dsDNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 
    0.277 (Depositor), 0.276 (DCC) 
  • R-Value Work: 
    0.243 (Depositor), 0.242 (DCC) 
  • R-Value Observed: 
    0.244 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 7WQ5

This is version 1.1 of the entry. See complete history

Literature

Molecular basis of the key regulator WRINKLED1 in plant oil biosynthesis.

Qiao, Z.Kong, Q.Tee, W.T.Lim, A.R.Q.Teo, M.X.Olieric, V.Low, P.M.Yang, Y.Qian, G.Ma, W.Gao, Y.G.

(2022) Sci Adv 8: eabq1211-eabq1211

  • DOI: https://doi.org/10.1126/sciadv.abq1211
  • Primary Citation Related Structures: 
    7WQ5

  • PubMed Abstract: 

    Vegetable oils are not only major components of human diet but also vital for industrial applications. WRINKLED1 (WRI1) is a pivotal transcription factor governing plant oil biosynthesis, but the underlying DNA-binding mechanism remains incompletely understood. Here, we resolved the structure of Arabidopsis WRI1 (AtWRI1) with its cognate double-stranded DNA (dsDNA), revealing two antiparallel β sheets in the tandem AP2 domains that intercalate into the adjacent major grooves of dsDNA to determine the sequence recognition specificity. We showed that AtWRI1 represented a previously unidentified structural fold and DNA-binding mode. Mutations of the key residues interacting with DNA element affected its binding affinity and oil biosynthesis when these variants were transiently expressed in tobacco leaves. Seed oil content was enhanced in stable transgenic wri1-1 expressing an AtWRI1 variant (W74R). Together, our findings offer a structural basis explaining WRI1 recognition and binding of DNA and suggest an alternative strategy to increase oil yield in crops through WRI1 bioengineering.


  • Organizational Affiliation
    • School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore.

Macromolecule Content 

  • Total Structure Weight: 87.9 kDa 
  • Atom Count: 4,652 
  • Modeled Residue Count: 426 
  • Deposited Residue Count: 600 
  • Unique protein chains: 1
  • Unique nucleic acid chains: 2

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Ethylene-responsive transcription factor WRI1
A, B
252Arabidopsis thalianaMutation(s): 0 
Gene Names: WRI1ASML1At3g54320T12E18.10T12E18.20
UniProt
Find proteins for Q6X5Y6 (Arabidopsis thaliana)
Explore Q6X5Y6 
Go to UniProtKB:  Q6X5Y6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6X5Y6
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(P*GP*TP*GP*GP*AP*CP*GP*AP*TP*GP*AP*AP*AP*CP*CP*GP*AP*GP*GP*AP*AP*GP*TP*A)-3')C [auth F],
E [auth D]
24Arabidopsis thaliana
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(P*TP*AP*CP*TP*TP*CP*CP*TP*CP*GP*GP*TP*TP*TP*CP*AP*TP*CP*GP*TP*CP*CP*AP*C)-3')D [auth C],
F [auth E]
24Arabidopsis thaliana
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NH4

Query on NH4



Download:Ideal Coordinates CCD File
G [auth D]AMMONIUM ION
H4 N
QGZKDVFQNNGYKY-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free:  0.277 (Depositor), 0.276 (DCC) 
  • R-Value Work:  0.243 (Depositor), 0.242 (DCC) 
  • R-Value Observed: 0.244 (Depositor) 
Space Group: C 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.52α = 90
b = 132.05β = 90
c = 124.43γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education (MoE, Singapore)Singapore--

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-31
    Type: Initial release
  • Version 1.1: 2024-05-29
    Changes: Data collection