5X4A

SLL-2-Forssman antigen tetrasaccharides complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.239 

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This is version 2.1 of the entry. See complete history


Literature

Crystal structure of octocoral lectin SLL-2 complexed with Forssman antigen tetrasaccharide.

Kita, A.Jimbo, M.Sakai, R.Morimoto, Y.Takeuchi, R.Tanaka, H.Takahashi, T.Miki, K.

(2017) Glycobiology 

  • DOI: https://doi.org/10.1093/glycob/cwx043
  • Primary Citation of Related Structures:  
    5X4A

  • PubMed Abstract: 

    A symbiosis-related lectin, SLL-2, from the octocoral Sinularia lochmodes, distributes densely on the cell surface of microalgae, Symbiodinium sp., an endosymbiotic dinoflagellate of the coral, and is also shown to be a chemical cue that transforms dinoflagellates into a nonmotile (coccoid) symbiotic state. SLL-2 binds to the sugar chain of the molecule similar to Forssman antigen pentasaccharide (GalNAcα1-3GalNAcβ1-3 Galα1-4 Galβ1-4Glc) on the surface of microalgae with high affinity. Here we report the crystal structure of the complex between SLL-2 and Forssman antigen tetrasaccharide (GalNAcα1-3GalNAcβ1-3 Galα1-4 Galβ) at 3.4 Å resolution. In an asymmetric unit of the crystal, there are two hexameric molecules with totally 12 sugar recognition sites. At 9 in 12 sites, the first and second saccharides of the Forssman antigen tetrasaccharide bind directly to galactopyranoside binding site of SLL-2, whereas the third and fourth saccharides have no interaction with the SLL-2 hexameric molecule that binds the first saccharide. The sugar chain bends at α-1,4-glycosidic linkage between the third and fourth saccharides toward the position that we defined as a pyranoside binding site in the crystal structure of the complex between SLL-2 and GalNAc. The structure allowed us to suggest a possible binding mode of the Forssman antigen pentasaccharide to SLL-2. These observations support our hypothesis that the binding of SLL-2 to the cell surface sugars of zooxanthella in a unique manner might trigger some physiological changes of the cell to adapt symbiosis with the host coral.


  • Organizational Affiliation

    Research Reactor Institute, Kyoto University, Kumatori, Sennan, Osaka 590-0494, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Galactose-binding lectin
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
94Sinularia lochmodesMutation(s): 0 
UniProt
Find proteins for A4CYJ6 (Sinularia lochmodes)
Explore A4CYJ6 
Go to UniProtKB:  A4CYJ6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA4CYJ6
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
BA [auth b],
CA [auth c],
EA [auth e],
GA [auth g],
M,
BA [auth b],
CA [auth c],
EA [auth e],
GA [auth g],
M,
O,
Q,
R,
T,
V,
X,
Z
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-3)-alpha-D-galactopyranose-(1-4)-beta-D-galactopyranose
AA [auth a],
DA [auth d],
FA [auth f],
HA [auth h],
N,
AA [auth a],
DA [auth d],
FA [auth f],
HA [auth h],
N,
P,
S,
U,
W,
Y
4N/A
Glycosylation Resources
GlyTouCan:  G88796WA
GlyCosmos:  G88796WA
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GLA
Query on GLA

Download Ideal Coordinates CCD File 
IA [auth A]alpha-D-galactopyranose
C6 H12 O6
WQZGKKKJIJFFOK-PHYPRBDBSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.239 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.468α = 90
b = 99.939β = 90
c = 273.936γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
JSPSJapan15K12750

Revision History  (Full details and data files)

  • Version 1.0: 2017-09-20
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary