Structure of SPH (Self-Incompatibility Protein Homologue) proteins, a widespread family of small, highly stable, secreted proteins from plants

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

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This is version 1.3 of the entry. See complete history


Structure of SPH (self-incompatibility protein homologue) proteins: a widespread family of small, highly stable, secreted proteins.

Rajasekar, K.V.Ji, S.Coulthard, R.J.Ride, J.P.Reynolds, G.L.Winn, P.J.Wheeler, M.J.Hyde, E.I.Smith, L.J.

(2019) Biochem J 476: 809-826

  • DOI: https://doi.org/10.1042/BCJ20180828
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    SPH (self-incompatibility protein homologue) proteins are a large family of small, disulfide-bonded, secreted proteins, initially found in the self-incompatibility response in the field poppy ( Papaver rhoeas ), but now known to be widely distributed in plants, many containing multiple members of this protein family. Using the Origami strain of Escherichia coli , we expressed one member of this family, SPH15 from Arabidopsis thaliana , as a folded thioredoxin fusion protein and purified it from the cytosol. The fusion protein was cleaved and characterised by analytical ultracentrifugation, circular dichroism and nuclear magnetic resonance (NMR) spectroscopy. This showed that SPH15 is monomeric and temperature stable, with a β-sandwich structure. The four strands in each sheet have the same topology as the unrelated proteins: human transthyretin, bacterial TssJ and pneumolysin, with no discernible sequence similarity. The NMR-derived structure was compared with a de novo model, made using a new deep learning algorithm based on co-evolution/correlated mutations, DeepCDPred, validating the method. The DeepCDPred de novo method and homology modelling to SPH15 were then both used to derive models of the 3D structure of the three known PrsS proteins from P. rhoeas , which have only 15-18% sequence homology to SPH15. The DeepCDPred method gave models with lower discreet optimised protein energy scores than the homology models. Three loops at one end of the poppy structures are postulated to interact with their respective pollen receptors to instigate programmed cell death in pollen tubes.

  • Organizational Affiliation

    Department of Biochemistry, University of Oxford, Oxford OX1 3QU, U.K.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
S-protein homolog 15115Arabidopsis thalianaMutation(s): 0 
Gene Names: SPH15At5g39493MUL8.19
Find proteins for Q9FLY6 (Arabidopsis thaliana)
Explore Q9FLY6 
Go to UniProtKB:  Q9FLY6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9FLY6
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom099185/Z/12/Z

Revision History  (Full details and data files)

  • Version 1.0: 2019-03-06
    Type: Initial release
  • Version 1.1: 2019-03-20
    Changes: Data collection, Database references
  • Version 1.2: 2019-05-08
    Changes: Data collection
  • Version 1.3: 2023-06-14
    Changes: Data collection, Database references, Other