7D3Y

Crystal structure of the osPHR2-osSPX2 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.11 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.222 

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This is version 1.2 of the entry. See complete history


Literature

Mechanistic insights into the regulation of plant phosphate homeostasis by the rice SPX2 - PHR2 complex.

Guan, Z.Zhang, Q.Zhang, Z.Zuo, J.Chen, J.Liu, R.Savarin, J.Broger, L.Cheng, P.Wang, Q.Pei, K.Zhang, D.Zou, T.Yan, J.Yin, P.Hothorn, M.Liu, Z.

(2022) Nat Commun 13: 1581-1581

  • DOI: https://doi.org/10.1038/s41467-022-29275-8
  • Primary Citation of Related Structures:  
    7D3T, 7D3Y

  • PubMed Abstract: 

    Phosphate (Pi) starvation response (PHR) transcription factors play key roles in plant Pi homeostasis maintenance. They are negatively regulated by stand-alone SPX proteins, cellular receptors for inositol pyrophosphate (PP-InsP) nutrient messengers. How PP-InsP-bound SPX interacts with PHRs is poorly understood. Here, we report crystal structures of the rice SPX2/InsP 6 /PHR2 complex and of the PHR2 DNA binding (MYB) domain in complex with target DNA at resolutions of 3.1 Å and 2.7 Å, respectively. In the SPX2/InsP 6 /PHR2 complex, the signalling-active SPX2 assembles into a domain-swapped dimer conformation and binds two copies of PHR2, targeting both its coiled-coil (CC) oligomerisation domain and MYB domain. Our results reveal that the SPX2 senses PP-InsPs to inactivate PHR2 by establishing severe steric clashes with the PHR2 MYB domain, preventing DNA binding, and by disrupting oligomerisation of the PHR2 CC domain, attenuating promoter binding. Our findings rationalize how PP-InsPs activate SPX receptor proteins to target PHR family transcription factors.


  • Organizational Affiliation

    National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SPX domain-containing protein 2,Isoform 1 of Core histone macro-H2A.1
A, B
394Oryza sativa Indica GroupHomo sapiens
This entity is chimeric
Mutation(s): 0 
Gene Names: SPX2OsI_06282MACROH2A1H2AFY
UniProt & NIH Common Fund Data Resources
Find proteins for O75367 (Homo sapiens)
Explore O75367 
Go to UniProtKB:  O75367
GTEx:  ENSG00000113648 
Find proteins for A2X254 (Oryza sativa subsp. indica)
Explore A2X254 
Go to UniProtKB:  A2X254
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsO75367A2X254
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Protein PHOSPHATE STARVATION RESPONSE 2
C, D, E
148Oryza sativa Japonica GroupMutation(s): 0 
Gene Names: PHR2Os07g0438800LOC_Os07g25710OSJNBa0026I22.19P0443H10.4
UniProt
Find proteins for Q6Z156 (Oryza sativa subsp. japonica)
Explore Q6Z156 
Go to UniProtKB:  Q6Z156
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6Z156
Sequence Annotations
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.11 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.222 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 147.812α = 90
b = 147.812β = 90
c = 143.287γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-10-06
    Type: Initial release
  • Version 1.1: 2022-05-04
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description