4YLD | pdb_00004yld

The crystal structure of Sclerotium Rolfsii lectin variant 1 (SSR1)

• PDB DOI: https://doi.org/10.2210/pdb4YLD/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Agroathelia rolfsii
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-03-05 Released: 2015-07-01 
• Deposition Author(s): Kantsadi, A.L., Peppa, V.I., Leonidas, D.D.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.179 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.147 (Depositor), 0.148 (DCC) 
• R-Value Observed: 
  0.148 (Depositor) 

Literature

Molecular Cloning, Carbohydrate Specificity and the Crystal Structure of Two Sclerotium rolfsii Lectin Variants.

Peppa, V.I., Venkat, H., Kantsadi, A.L., Inamdar, S.R., Bhat, G.G., Eligar, S., Shivanand, A., Chachadi, V.B., Satisha, G.J., Swamy, B.M., Skamnaki, V.T., Zographos, S.E., Leonidas, D.D.

(2015) Molecules 20: 10848-10865

• PubMed: 26076107 
• DOI: https://doi.org/10.3390/molecules200610848
• Primary Citation Related Structures: 
  4YLD, 4Z2F, 4Z2Q, 4Z2S


• PubMed Abstract: 
  

  SRL is a cell wall associated developmental-stage specific lectin secreted by Sclerotium rolfsii, a soil-born pathogenic fungus. SRL displays specificity for TF antigen (Galβ1→3GalNAc-α-Ser//Thr) expressed in all cancer types and has tumour suppressing effects in vivo. Considering the immense potential of SRL in cancer research, we have generated two variant gene constructs of SRL and expressed in E. coli to refine the sugar specificity and solubility by altering the surface charge. SSR1 and SSR2 are two different recombinant variants of SRL, both of which recognize TF antigen but only SSR1 binds to Tn antigen (GalNAcα-Ser/Thr). The glycan array analysis of the variants demonstrated that SSR1 recognizes TF antigen and their derivative with high affinity similar to SRL but showed highest affinity towards the sialylated Tn antigen, unlike SRL. The carbohydrate binding property of SSR2 remains unaltered compared to SRL. The crystal structures of the two variants were determined in free form and in complex with N-acetylglucosamine at 1.7 Å and 1.6 Å resolution, respectively. Structural analysis highlighted the structural basis of the fine carbohydrate specificity of the two SRL variants and results are in agreement with glycan array analysis.

---

Organizational Affiliation: 
• Department of Biochemistry and Biotechnology, University of Thessaly, 26 Ploutonos Street, Larissa 41221, Greece. [e-mail].
Department of Biochemistry, Kuvempu University, Shimoga, Karnataka 577451, India. [e-mail].
Department of Biochemistry and Biotechnology, University of Thessaly, 26 Ploutonos Street, Larissa 41221, Greece. [e-mail].
Department of Post Graduate Studies in Biochemistry, Karnatak University, Dharwad 580003, India. [e-mail].
Department of Post Graduate Studies in Biochemistry, Karnatak University, Dharwad 580003, India. [e-mail].
Department of Post Graduate Studies in Biochemistry, Karnatak University, Dharwad 580003, India. [e-mail].
Department of Post Graduate Studies in Biochemistry, Karnatak University, Dharwad 580003, India. [e-mail].
Department of Post Graduate Studies in Biochemistry, Karnatak University, Dharwad 580003, India. [e-mail].
Department of Biochemistry, Kuvempu University, Shimoga, Karnataka 577451, India. [e-mail].
Department of Post Graduate Studies in Biochemistry, Karnatak University, Dharwad 580003, India. [e-mail].
Department of Biochemistry and Biotechnology, University of Thessaly, 26 Ploutonos Street, Larissa 41221, Greece. [e-mail].
Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, 48 Vas. Constantinou Ave, Athens 11635, Greece. [e-mail].
Department of Biochemistry and Biotechnology, University of Thessaly, 26 Ploutonos Street, Larissa 41221, Greece. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 32.24 kDa 
• Atom Count: 2,682 
• Modeled Residue Count: 282 
• Deposited Residue Count: 282 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sclerotium Rolfsii lectin variant 1 (SSR1)	A, B	141	Agroathelia rolfsii	Mutation(s): 0
UniProt
Find proteins for A0A0M3KL30 (Agroathelia rolfsii) Explore A0A0M3KL30  Go to UniProtKB:  A0A0M3KL30

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD	C [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.179 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.147 (Depositor), 0.148 (DCC) 
• R-Value Observed: 0.148 (Depositor) 

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.285	α = 90
b = 100.285	β = 90
c = 63.643	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CrysalisPro	data reduction
SCALA	data scaling
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-07-01 
Deposition Author(s): Kantsadi, A.L., Peppa, V.I., Leonidas, D.D.

Revision History  

• Version 1.0: 2015-07-01
  Type: Initial release
  
• Version 1.1: 2024-05-01
  Changes: Data collection, Database references, Refinement description