7QE3 | pdb_00007qe3

Se-M variant of B-trefoil lectin from Salpingoeca rosetta in complex with GalNAc


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.231 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.182 (Depositor), 0.190 (DCC) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

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This is version 1.2 of the entry. See complete history


Literature

The choanoflagellate pore-forming lectin SaroL-1 punches holes in cancer cells by targeting the tumor-related glycosphingolipid Gb3.

Notova, S.Bonnardel, F.Rosato, F.Siukstaite, L.Schwaiger, J.Lim, J.H.Bovin, N.Varrot, A.Ogawa, Y.Romer, W.Lisacek, F.Imberty, A.

(2022) Commun Biol 5: 954-954

  • DOI: https://doi.org/10.1038/s42003-022-03869-w
  • Primary Citation of Related Structures:  
    7QE3, 7QE4, 7R55

  • PubMed Abstract: 

    Choanoflagellates are primitive protozoa used as models for animal evolution. They express a large variety of multi-domain proteins contributing to adhesion and cell communication, thereby providing a rich repertoire of molecules for biotechnology. Adhesion often involves proteins adopting a β-trefoil fold with carbohydrate-binding properties therefore classified as lectins. Sequence database screening with a dedicated method resulted in TrefLec, a database of 44714 β-trefoil candidate lectins across 4497 species. TrefLec was searched for original domain combinations, which led to single out SaroL-1 in the choanoflagellate Salpingoeca rosetta, that contains both β-trefoil and aerolysin-like pore-forming domains. Recombinant SaroL-1 is shown to bind galactose and derivatives, with a stronger affinity for cancer-related α-galactosylated epitopes such as the glycosphingolipid Gb3, when embedded in giant unilamellar vesicles or cell membranes. Crystal structures of complexes with Gb3 trisaccharide and GalNAc provided the basis for building a model of the oligomeric pore. Finally, recognition of the αGal epitope on glycolipids required for hemolysis of rabbit erythrocytes suggests that toxicity on cancer cells is achieved through carbohydrate-dependent pore-formation.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sarol-1A [auth AAA],
B [auth BBB]
350Salpingoeca rosettaMutation(s): 0 
Gene Names: PTSG_08235
UniProt
Find proteins for F2UID9 (Salpingoeca rosetta (strain ATCC 50818 / BSB-021))
Explore F2UID9 
Go to UniProtKB:  F2UID9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF2UID9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NGA (Subject of Investigation/LOI)
Query on NGA

Download Ideal Coordinates CCD File 
C [auth AAA]2-acetamido-2-deoxy-beta-D-galactopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-JAJWTYFOSA-N
PGE
Query on PGE

Download Ideal Coordinates CCD File 
J [auth BBB]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
1JW
Query on 1JW

Download Ideal Coordinates CCD File 
F [auth BBB],
G [auth BBB],
H [auth BBB]
(2S)-hexane-1,2,6-triol
C6 H14 O3
ZWVMLYRJXORSEP-LURJTMIESA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
E [auth AAA]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
D [auth AAA],
I [auth BBB],
K [auth BBB]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A [auth AAA],
B [auth BBB]
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.231 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.182 (Depositor), 0.190 (DCC) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.99α = 90
b = 58.579β = 90.682
c = 166.424γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
SHELXmodel building
SHELXphasing
CRANK2phasing
BUCCANEERmodel building

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NGAClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
H2020 Marie Curie Actions of the European CommissionEuropean Union814029

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-14
    Type: Initial release
  • Version 1.1: 2022-09-28
    Changes: Database references
  • Version 1.2: 2024-10-16
    Changes: Data collection, Structure summary