Crystal Structure Of Soybean beta-Conglycinin Beta Homotrimer (I122M/K124W)

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.221 

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Creation of soybean beta-conglycinin beta with strong phagocytosis-stimulating activity

Maruyama, N.Maruyama, Y.Tsuruki, T.Okuda, E.Yoshikawa, M.Utsumi, S.

(2003) Biochim Biophys Acta 1648: 99-104

  • DOI: https://doi.org/10.1016/s1570-9639(03)00113-4
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    beta-Conglycinin is composed of three kinds of subunit: alpha, alpha' and beta. A phagocytosis-stimulating peptide sequence (MITLAIPVNKPGR), soymetide, exists in the alpha' subunit of beta-conglycinin. Met at N terminus of the soymetide is essential for the activity. When Thr at the third residue from N terminus of the soymetide is replaced by Phe or Trp, the phagocytosis-stimulating activity greatly increases (ThrMet, Lys-->Thr, Phe, or Trp) into the beta subunit after confirmation of the effects of residue replacements by molecular modeling, suggesting that the introduced mutations might not prevent the correct folding. The studies of circular dichroism (CD), gel filtration and differential scanning calorimetry (DSC) of the mutants (I122M/K124T, I122M/K124F, I122M/K124W) expressed in E. coli demonstrated that they folded and self-assembled similarly to the wild type. This was confirmed by X-ray analysis of I122M/K124W crystal where the biggest residue tryptophane was introduced. The three mutants exhibited phagocytosis activities after digestion by trypsin, and the order was the wild type

  • Organizational Affiliation

    Laboratory of Food Quality Design and Development, Graduate School of Agriculture, Kyoto University, Uji, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
beta subunit of beta conglycinin
A, B, C, D, E
A, B, C, D, E, F
416Glycine maxMutation(s): 2 
Find proteins for P25974 (Glycine max)
Explore P25974 
Go to UniProtKB:  P25974
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25974
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.50 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.221 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 130.263α = 90
b = 62.583β = 90.44
c = 159.009γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
HKL-2000data reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-07-16
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-11-10
    Changes: Database references
  • Version 1.4: 2023-12-27
    Changes: Data collection