9UDY | pdb_00009udy

Crystal structure of recombinant mushroom Agaricus bisporus mannose-binding protein with a longer C-terminal region


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.51 Å
  • R-Value Free: 
    0.194 (Depositor), 0.201 (DCC) 
  • R-Value Work: 
    0.132 (Depositor), 0.145 (DCC) 
  • R-Value Observed: 
    0.135 (Depositor) 

Starting Model: experimental
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Literature

Crystal structure of a recombinant Agaricus bisporus mushroom mannose-binding protein with a longer C-terminal region.

Yoshida, H.Nakakita, S.I.Rachmawati, H.Tjandrawinata, R.R.Ismaya, W.T.

(2025) Acta Crystallogr F Struct Biol Commun 81: 241-248

  • DOI: https://doi.org/10.1107/S2053230X25003905
  • Primary Citation of Related Structures:  
    9UDY, 9UDZ

  • PubMed Abstract: 

    A lectin-like protein was discovered in Agaricus bisporus as part of the mushroom tyrosinase complex. The protein has a β-trefoil fold, which is typical of the ricin B-like-type lectin family. The structure of the recombinant protein has been elucidated, and its specific sugar-binding affinity towards mannose and mannitol has also been reported; therefore, the protein was named A. bisporus mannose-binding protein (Abmb). Although the sugar-binding site of Abmb is predicted to be close to the C-terminus, the sugar-binding site has not yet been determined. In this study, a variant of recombinant Abmb with a longer C-terminal region including a 6×His-tag was constructed and its structure was solved at 1.51 and 2.34 Å resolution in an orthorhombic and a monoclinic space group, respectively. The overall structure showed a β-trefoil fold as previously reported; however, several surface loop regions including the C-terminal region showed high flexibility. In addition, a glycan-search assay of this variant showed weak binding affinity towards β-D-galactose but no affinity towards α-D-mannose. The plasticity of the C-terminal tail could be related to the differences in the carbohydrate-binding affinity of Abmb.


  • Organizational Affiliation
    • Department of Basic Life Science, Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0793, Japan.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lectin-like fold protein170Agaricus bisporusMutation(s): 0 
UniProt
Find proteins for G1K3P4 (Agaricus bisporus)
Explore G1K3P4 
Go to UniProtKB:  G1K3P4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG1K3P4
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TRS
Query on TRS

Download Ideal Coordinates CCD File 
B [auth A]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.51 Å
  • R-Value Free:  0.194 (Depositor), 0.201 (DCC) 
  • R-Value Work:  0.132 (Depositor), 0.145 (DCC) 
  • R-Value Observed: 0.135 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.164α = 90
b = 43.982β = 90
c = 67.247γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not fundedJapan--

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-21
    Type: Initial release
  • Version 1.1: 2025-06-11
    Changes: Database references