6FX1

Crystal structure of Pholiota squarrosa lectin in complex with an octasaccharide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 

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This is version 2.0 of the entry. See complete history


Literature

Recognition of Complex Core-Fucosylated N-Glycans by a Mini Lectin.

Cabanettes, A.Perkams, L.Spies, C.Unverzagt, C.Varrot, A.

(2018) Angew Chem Int Ed Engl 57: 10178-10181

  • DOI: 10.1002/anie.201805165
  • Primary Citation of Related Structures:  
    6EKE, 6FX1, 6FX2, 6FX3

  • PubMed Abstract: 
  • The mini fungal lectin PhoSL was recombinantly produced and characterized. Despite a length of only 40 amino acids, PhoSL exclusively recognizes N-glycans with α1,6-linked fucose. Core fucosylation influences the intrinsic properties and bioactivities of mammalian N-glycoproteins and its level is linked to various cancers ...

    The mini fungal lectin PhoSL was recombinantly produced and characterized. Despite a length of only 40 amino acids, PhoSL exclusively recognizes N-glycans with α1,6-linked fucose. Core fucosylation influences the intrinsic properties and bioactivities of mammalian N-glycoproteins and its level is linked to various cancers. Thus, PhoSL serves as a promising tool for glycoprofiling. Without structural precedence, the crystal structure was solved using the zinc anomalous signal, and revealed an interlaced trimer creating a novel protein fold termed β-prism III. Three biantennary core-fucosylated N-glycan azides of 8 to 12 sugars were cocrystallized with PhoSL. The resulting highly resolved structures gave a detailed view on how the exclusive recognition of α1,6-fucosylated N-glycans by such a small protein occurs. This work also provided a protein consensus motif for the observed specificity as well as a glimpse into N-glycan flexibility upon binding.


    Organizational Affiliation

    Univ. Grenoble Alpes, CNRS, CERMAV, 38000, Grenoble, France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
lectin
A, B, C, D, E, F, G, H
A, B, C, D, E, F, G, H, I, J, K, L
43Pholiota squarrosaMutation(s): 0 
UniProt
Find proteins for A0A3B6UEU4 (Pholiota squarrosa)
Explore A0A3B6UEU4 
Go to UniProtKB:  A0A3B6UEU4
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]1-azido-beta-N-acetyl-D-glucosamineM, O, R, X6N/AN/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G53233QZ
GlyCosmos:  G53233QZ
Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]1-azido-beta-N-acetyl-D-glucosamineN, U8N/AN/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G12228DK
GlyCosmos:  G12228DK
Entity ID: 4
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]1-azido-beta-N-acetyl-D-glucosamineP5N/AN/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G15526KS
GlyCosmos:  G15526KS
Entity ID: 5
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]1-azido-beta-N-acetyl-D-glucosamineQ, S7N/AN/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G70122IR
GlyCosmos:  G70122IR
Entity ID: 6
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]1-azido-beta-N-acetyl-D-glucosamineT, V, W4N/AN/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G02611HY
GlyCosmos:  G02611HY
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 
  • Space Group: P 21 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91α = 90
b = 95.593β = 90
c = 110.633γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-07-11
    Type: Initial release
  • Version 1.1: 2018-07-18
    Changes: Data collection, Structure summary
  • Version 1.2: 2018-08-29
    Changes: Data collection, Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary