7D3T

Crystal structure of OSPHR2 in complex with DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.215 

wwPDB Validation   3D Report Full Report


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

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein PHOSPHATE STARVATION RESPONSE 2
A, B, C, D
144Oryza sativa Indica GroupMutation(s): 0 
Gene Names: PHR2OsI_25821
UniProt
Find proteins for B8B5N8 (Oryza sativa subsp. indica)
Explore B8B5N8 
Go to UniProtKB:  B8B5N8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB8B5N8
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(P*GP*CP*TP*TP*GP*AP*GP*GP*AP*TP*AP*TP*CP*CP*GP*A)-3')
E, G
16synthetic construct
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(P*CP*TP*CP*GP*GP*AP*TP*AP*TP*CP*CP*TP*CP*AP*AP*G)-3')
F, H
16synthetic construct
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.215 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.414α = 90
b = 100.824β = 102.456
c = 79.351γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



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