5GZE

Galectin-8 N-terminal domain carbohydrate recognition domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.32 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.253 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Crystallization of Galectin-8 Linker Reveals Intricate Relationship between the N-terminal Tail and the Linker.

Si, Y.Wang, Y.Gao, J.Song, C.Feng, S.Zhou, Y.Tai, G.Su, J.

(2016) Int J Mol Sci 17

  • DOI: 10.3390/ijms17122088
  • Primary Citation of Related Structures:  
    5GZC, 5GZE, 5GZD, 5GZG, 5GZF

  • PubMed Abstract: 
  • Galectin-8 (Gal-8) plays a significant role in normal immunological function as well as in cancer. This lectin contains two carbohydrate recognition domains (CRD) connected by a peptide linker. The N-terminal CRD determines ligand binding specificity, whereas the linker has been proposed to regulate overall Gal-8 function, including multimerization and biological activity ...

    Galectin-8 (Gal-8) plays a significant role in normal immunological function as well as in cancer. This lectin contains two carbohydrate recognition domains (CRD) connected by a peptide linker. The N-terminal CRD determines ligand binding specificity, whereas the linker has been proposed to regulate overall Gal-8 function, including multimerization and biological activity. Here, we crystallized the Gal-8 N-terminal CRD with the peptide linker using a crystallization condition that contains Ni 2+ . The Ni 2+ ion was found to be complexed between two CRDs via crystal packing contacts. The coordination between Ni 2+ and Asp25 plays an indirect role in determining the structure of β-strand F0 and in influencing the linker conformation which could not be defined due to its dynamic nature. The linker was also shortened in situ and crystallized under a different condition, leading to a higher resolution structure refined to 1.08 Å. This crystal structure allowed definition of a short portion of the linker interacting with the Gal-8 N-terminal tail via ionic interactions and hydrogen bonds. Observation of two Gal-8 N-terminal CRD structures implies that the N-terminal tail and the linker may influence each other's conformation. In addition, under specific crystallization conditions, glycerol could replace lactose and was observed at the carbohydrate binding site. However, glycerol did not show inhibition activity in hemagglutination assay.


    Organizational Affiliation

    Jilin Province Key Laboratory on Chemistry and Biology of Natural Drugs in Changbai Mountain, School of Life Sciences, Northeast Normal University, Changchun 130024, China. sujy100@nenu.edu.cn.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Galectin-8A148Homo sapiensMutation(s): 0 
Gene Names: LGALS8
UniProt & NIH Common Fund Data Resources
Find proteins for O00214 (Homo sapiens)
Explore O00214 
Go to UniProtKB:  O00214
PHAROS:  O00214
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-galactopyranose-(1-4)-beta-D-glucopyranoseB2N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G84224TW
GlyCosmos:  G84224TW
GlyGen:  G84224TW
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
LAT BindingDB:  5GZE Kd: 6.20e+4 (nM) from 1 assay(s)
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900004
Query on PRD_900004
Bbeta-lactoseOligosaccharide /  Nutrient Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.32 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.253 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.687α = 90
b = 39.744β = 108.02
c = 55.802γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

  • Deposited Date: 2016-09-28 
  • Released Date: 2016-12-21 
  • Deposition Author(s): Su, J.Y., Si, Y.L.

Revision History  (Full details and data files)

  • Version 1.0: 2016-12-21
    Type: Initial release
  • Version 1.1: 2019-12-25
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary