2P1Q

Mechanism of Auxin Perception by the TIR1 ubiquitin ligase

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Mechanism of auxin perception by the TIR1 ubiquitin ligase.

Tan, X., Calderon-Villalobos, L.I., Sharon, M., Zheng, C., Robinson, C.V., Estelle, M., Zheng, N.

(2007) Nature 446: 640-645

  • DOI: 10.1038/nature05731
  • Primary Citation of Related Structures:  
    2P1Q, 2P1P, 2P1O, 2P1N, 2P1M

  • PubMed Abstract: 

    • Auxin is a pivotal plant hormone that controls many aspects of plant growth and development. Perceived by a small family of F-box proteins including transport inhibitor response 1 (TIR1), auxin regulates gene expression by promoting SCF ubiquitin-ligase-catalysed degradation of the Aux/IAA transcription repressors, but how the TIR1 F-box protein senses and becomes activated by auxin remains unclear ...

    Auxin is a pivotal plant hormone that controls many aspects of plant growth and development. Perceived by a small family of F-box proteins including transport inhibitor response 1 (TIR1), auxin regulates gene expression by promoting SCF ubiquitin-ligase-catalysed degradation of the Aux/IAA transcription repressors, but how the TIR1 F-box protein senses and becomes activated by auxin remains unclear. Here we present the crystal structures of the Arabidopsis TIR1-ASK1 complex, free and in complexes with three different auxin compounds and an Aux/IAA substrate peptide. These structures show that the leucine-rich repeat domain of TIR1 contains an unexpected inositol hexakisphosphate co-factor and recognizes auxin and the Aux/IAA polypeptide substrate through a single surface pocket. Anchored to the base of the TIR1 pocket, auxin binds to a partially promiscuous site, which can also accommodate various auxin analogues. Docked on top of auxin, the Aux/IAA substrate peptide occupies the rest of the TIR1 pocket and completely encloses the hormone-binding site. By filling in a hydrophobic cavity at the protein interface, auxin enhances the TIR1-substrate interactions by acting as a 'molecular glue'. Our results establish the first structural model of a plant hormone receptor.

    Organizational Affiliation: 

    Department of Pharmacology, University of Washington, School of Medicine, Box 357280, Seattle, Washington 98195, USA.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SKP1-like protein 1A A160Arabidopsis thalianaMutation(s): 0 
Gene Names: SKP1A, ASK1, SKP1, UIP1, At1g75950, T4O12.17
Find proteins for Q39255 (Arabidopsis thaliana)
Explore Q39255 
Go to UniProtKB:  Q39255
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
TRANSPORT INHIBITOR RESPONSE 1 protein B594Arabidopsis thalianaMutation(s): 0 
Gene Names: TIR1, FBL1, WEI1, At3g62980, T20O10.80
Find proteins for Q570C0 (Arabidopsis thaliana)
Explore Q570C0 
Go to UniProtKB:  Q570C0
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Auxin-responsive protein IAA7 C13N/AMutation(s): 0 
Find proteins for Q38825 (Arabidopsis thaliana)
Explore Q38825 
Go to UniProtKB:  Q38825
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IHP
Query on IHP
Download Ideal Coordinates CCD File 
B
INOSITOL HEXAKISPHOSPHATE
C6 H18 O24 P6
IMQLKJBTEOYOSI-GPIVLXJGSA-N		 Ligand Interaction
IAC
Query on IAC
Download Ideal Coordinates CCD File 
B
1H-INDOL-3-YLACETIC ACID
C10 H9 N O2
SEOVTRFCIGRIMH-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.207α = 90
b = 82.472β = 104.05
c = 125.053γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-04-10
    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: 2020-10-14
    Changes: Derived calculations, Structure summary