7DJL

Structure of four truncated and mutated forms of quenching protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.96 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.171 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of Arabidopsis SOQ1 lumenal region unveils C-terminal domain essential for negative regulation of photoprotective qH.

Yu, G.Hao, J.Pan, X.Shi, L.Zhang, Y.Wang, J.Fan, H.Xiao, Y.Yang, F.Lou, J.Chang, W.Malnoe, A.Li, M.

(2022) Nat Plants 8: 840-855

  • DOI: https://doi.org/10.1038/s41477-022-01177-z
  • Primary Citation of Related Structures:  
    7DJJ, 7DJK, 7DJL, 7DJM

  • PubMed Abstract: 

    Non-photochemical quenching (NPQ) plays an important role for phototrophs in decreasing photo-oxidative damage. qH is a sustained form of NPQ and depends on the plastid lipocalin (LCNP). A thylakoid membrane-anchored protein SUPPRESSOR OF QUENCHING1 (SOQ1) prevents qH formation by inhibiting LCNP. SOQ1 suppresses qH with its lumen-located thioredoxin (Trx)-like and NHL domains. Here we report structural data, genetic modification and biochemical characterization of Arabidopsis SOQ1 lumenal domains. Our results show that the Trx-like and NHL domains are associated together, with the cysteine motif located at their interface. Residue E859, required for SOQ1 function, is pivotal for maintaining the Trx-NHL association. Importantly, the C-terminal region of SOQ1 forms an independent β-stranded domain that has structural homology to the N-terminal domain of bacterial disulfide bond protein D and is essential for negative regulation of qH. Furthermore, SOQ1 is susceptible to cleavage at the loops connecting the neighbouring lumenal domains both in vitro and in vivo, which could be a regulatory process for its suppression function of qH.


  • Organizational Affiliation

    National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, P.R. China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein SUPPRESSOR OF QUENCHING 1, chloroplasticA [auth C],
B [auth A],
C [auth B]
498Arabidopsis thalianaMutation(s): 1 
Gene Names: SOQ1At1g56500F13N6.21
EC: 3.1.3
UniProt
Find proteins for Q8VZ10 (Arabidopsis thaliana)
Explore Q8VZ10 
Go to UniProtKB:  Q8VZ10
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8VZ10
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.96 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.171 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 153.933α = 90
b = 166.298β = 116.824
c = 95.74γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China2016YFA0502900
Ministry of Science and Technology (MoST, China)China2017YFA0503702
Chinese Academy of SciencesChinaXDB27020106
National Natural Science Foundation of China (NSFC)China31600609
National Natural Science Foundation of China (NSFC)China31770778
Chinese Academy of SciencesChina2018128

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-08
    Type: Initial release
  • Version 1.1: 2022-12-21
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description