6ZV5

CML1 crystal structure in complex with Lewis a tetrasaccharide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.187 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structure-function relationship of a novel fucoside-binding fruiting body lectin from Coprinopsis cinerea exhibiting nematotoxic activity.

Bleuler-Martinez, S.Varrot, A.Olieric, V.Schubert, M.Vogt, E.Fetz, C.Wohlschlager, T.Plaza, D.F.Walti, M.Duport, Y.Capitani, G.Aebi, M.Kunzler, M.

(2022) Glycobiology 32: 600-615

  • DOI: https://doi.org/10.1093/glycob/cwac020
  • Primary Citation of Related Structures:  
    6ZRW, 6ZU2, 6ZV5

  • PubMed Abstract: 

    Lectins are non-immunoglobulin-type proteins that bind to specific carbohydrate epitopes and play important roles in intra- and inter-organismic interactions. Here, we describe a novel fucose-specific lectin, termed CML1, which we identified from fruiting body extracts of Coprinopsis cinerea. For further characterization, the coding sequence for CML1 was cloned and heterologously expressed in Escherichia coli. Feeding of CML1-producing bacteria inhibited larval development of the bacterivorous nematode Caenorhabditis tropicalis, but not of C. elegans. The crystal structure of the recombinant protein in its apo-form and in complex with H type I or Lewis A blood group antigens was determined by X-ray crystallography. The protein folds as a sandwich of 2 antiparallel β-sheets and forms hexamers resulting from a trimer of dimers. The hexameric arrangement was confirmed by small-angle X-ray scattering (SAXS). One carbohydrate-binding site per protomer was found at the dimer interface with both protomers contributing to ligand binding, resulting in a hexavalent lectin. In terms of lectin activity of recombinant CML1, substitution of the carbohydrate-interacting residues His54, Asn55, Trp94, and Arg114 by Ala abolished carbohydrate-binding and nematotoxicity. Although no similarities to any characterized lectin were found, sequence alignments identified many non-characterized agaricomycete proteins. These results suggest that CML1 is the founding member of a novel family of fucoside-binding lectins involved in the defense of agaricomycete fruiting bodies against predation by fungivorous nematodes.


  • Organizational Affiliation

    Institute of Microbiology, Department of Biology, Eidgenössische Technische Hochschule (ETH) Zürich, 8093, Zürich, Switzerland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mucin-binding lectin 1126Coprinopsis cinereaMutation(s): 0 
Gene Names: cml1
UniProt
Find proteins for B3VS76 (Coprinopsis cinerea)
Explore B3VS76 
Go to UniProtKB:  B3VS76
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB3VS76
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-galactopyranose-(1-3)-[alpha-L-fucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranoseG [auth AaA],
H [auth BaB],
K [auth EaE],
L [auth FaF]
3N/A
Glycosylation Resources
GlyTouCan:  G39023AU
GlyCosmos:  G39023AU
GlyGen:  G39023AU
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-galactopyranose-(1-3)-[alpha-L-fucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-alpha-D-galactopyranoseI [auth CaC],
J [auth DaD]
4N/A
Glycosylation Resources
GlyTouCan:  G13393XR
GlyCosmos:  G13393XR
GlyGen:  G13393XR
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
M [auth BBB]
N [auth CCC]
O [auth DDD]
P [auth DDD]
Q [auth DDD]
M [auth BBB],
N [auth CCC],
O [auth DDD],
P [auth DDD],
Q [auth DDD],
R [auth EEE],
S [auth FFF],
T [auth FFF],
U [auth FFF],
V [auth FFF],
W [auth FFF]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.187 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.925α = 90
b = 73.925β = 90
c = 119.592γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Research AgencyFranceANR-15-IDEX- 02
Swiss National Science FoundationSwitzerland31003A_173097

Revision History  (Full details and data files)

  • Version 1.0: 2021-08-04
    Type: Initial release
  • Version 1.1: 2022-02-09
    Changes: Database references
  • Version 1.2: 2022-04-06
    Changes: Database references
  • Version 1.3: 2022-06-22
    Changes: Database references, Derived calculations
  • Version 1.4: 2024-01-31
    Changes: Data collection, Refinement description