5XG5 | pdb_00005xg5

Crystal structure of Mitsuba-1 with bound NAcGal

• PDB DOI: https://doi.org/10.2210/pdb5XG5/pdb

• Classification: DE NOVO PROTEIN
• Organism(s): synthetic construct
• Mutation(s): No 


• Deposited: 2017-04-12 Released: 2017-07-12 
• Deposition Author(s): Terada, D., Voet, A.R.D., Kamata, K., Zhang, K.Y.J., Tame, J.R.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free: 
  0.197 (Depositor), 0.207 (DCC) 
• R-Value Work: 
  0.150 (Depositor), 0.162 (DCC) 
• R-Value Observed: 
  0.152 (Depositor) 

Literature

Computational design of a symmetrical beta-trefoil lectin with cancer cell binding activity.

Terada, D., Voet, A.R.D., Noguchi, H., Kamata, K., Ohki, M., Addy, C., Fujii, Y., Yamamoto, D., Ozeki, Y., Tame, J.R.H., Zhang, K.Y.J.

(2017) Sci Rep 7: 5943-5943

• PubMed: 28724971 
• DOI: https://doi.org/10.1038/s41598-017-06332-7
• Primary Citation Related Structures: 
  5XG5


• PubMed Abstract: 
  

  Computational protein design has advanced very rapidly over the last decade, but there remain few examples of artificial proteins with direct medical applications. This study describes a new artificial β-trefoil lectin that recognises Burkitt's lymphoma cells, and which was designed with the intention of finding a basis for novel cancer treatments or diagnostics. The new protein, called "Mitsuba", is based on the structure of the natural shellfish lectin MytiLec-1, a member of a small lectin family that uses unique sequence motifs to bind α-D-galactose. The three subdomains of MytiLec-1 each carry one galactose binding site, and the 149-residue protein forms a tight dimer in solution. Mitsuba (meaning "three-leaf" in Japanese) was created by symmetry constraining the structure of a MytiLec-1 subunit, resulting in a 150-residue sequence that contains three identical tandem repeats. Mitsuba-1 was expressed and crystallised to confirm the X-ray structure matches the predicted model. Mitsuba-1 recognises cancer cells that express globotriose (Galα(1,4)Galβ(1,4)Glc) on the surface, but the cytotoxicity is abolished.

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Organizational Affiliation: 
• Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro, Yokohama, Kanagawa, 230-0045, Japan.
Structural Bioinformatics Team, Division of Structural and Synthetic Biology, Center for Life Science Technologies, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan.
Laboratory of Biomolecular Modelling and Design, Department of Chemistry, KU Leuven, Celestijnenlaan 200G, 3001, Heverlee, Belgium.
Department of Pharmacy, Graduate School of Pharmaceutical Science, Nagasaki International University, 2825-7 Huis Ten Bosch, Sasebo, Nagasaki, 859-3298, Japan.
Laboratory of Glycobiology and Marine Biochemistry, Graduate School of NanoBio Sciences, Yokohama City University, 22-2, Seto, Yokohama, Kanagawa, 236-0027, Japan.
Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro, Yokohama, Kanagawa, 230-0045, Japan. [e-mail].
Structural Bioinformatics Team, Division of Structural and Synthetic Biology, Center for Life Science Technologies, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 17.11 kDa 
• Atom Count: 1,338 
• Modeled Residue Count: 145 
• Deposited Residue Count: 145 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MITSUBA-1	A	145	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A2G	B [auth A], C [auth A], D [auth A]	2-acetamido-2-deoxy-alpha-D-galactopyranose C8 H15 N O6 OVRNDRQMDRJTHS-CBQIKETKSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free:  0.197 (Depositor), 0.207 (DCC) 
• R-Value Work:  0.150 (Depositor), 0.162 (DCC) 
• R-Value Observed: 0.152 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.782	α = 90
b = 38.677	β = 97.56
c = 42.761	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-07-12 
Deposition Author(s): Terada, D., Voet, A.R.D., Kamata, K., Zhang, K.Y.J., Tame, J.R.H.

Revision History  

• Version 1.0: 2017-07-12
  Type: Initial release
  
• Version 1.1: 2017-08-30
  Changes: Data collection, Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-03-27
  Changes: Data collection, Database references, Structure summary