5FSB | pdb_00005fsb

Structure of tectonin 2 from laccaria bicolor in complex with 2-o-methyl-methyl-seleno-beta-l-fucopyranoside


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 
    0.167 (Depositor), 0.180 (DCC) 
  • R-Value Work: 
    0.133 (Depositor), 0.150 (DCC) 
  • R-Value Observed: 
    0.135 (Depositor) 

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Ligand Structure Quality Assessment 

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This is version 1.4 of the entry. See complete history


Literature

Crystal Structures of Fungal Tectonin in Complex with O-Methylated Glycans Suggest Key Role in Innate Immune Defense.

Sommer, R.Makshakova, O.N.Wohlschlager, T.Hutin, S.Marsh, M.Titz, A.Kunzler, M.Varrot, A.

(2018) Structure 26: 391-402.e4

  • DOI: https://doi.org/10.1016/j.str.2018.01.003
  • Primary Citation of Related Structures:  
    5FSB, 5FSC

  • PubMed Abstract: 

    Innate immunity is the first line of defense against pathogens and predators. To initiate a response, it relies on the detection of invaders, where lectin-carbohydrate interactions play a major role. O-Methylated glycans were previously identified as non-self epitopes and conserved targets for defense effector proteins belonging to the tectonin superfamily. Here, we present two crystal structures of Tectonin 2 from the mushroom Laccaria bicolor in complex with methylated ligands, unraveling the molecular basis for this original specificity. Furthermore, they revealed the formation of a ball-shaped tetramer with 24 binding sites distributed at its surface, resembling a small virus capsid. Based on the crystal structures, a methylation recognition motif was identified and found in the sequence of many tectonins from bacteria to human. Our results support a key role of tectonins in innate defense based on a distinctive and conserved type of lectin-glycan interaction.


  • Organizational Affiliation

    Chemical Biology of Carbohydrates, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), 66123 Saarbrücken, Germany; Deutsches Zentrum für Infektionsforschung, Standort Hannover-Braunschweig, Hannover, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TECTONIN 2
A, B
227Laccaria bicolor S238N-H82Mutation(s): 0 
UniProt
Find proteins for B0CZL6 (Laccaria bicolor (strain S238N-H82 / ATCC MYA-4686))
Explore B0CZL6 
Go to UniProtKB:  B0CZL6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB0CZL6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
6YR
Query on 6YR

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
methyl 1-seleno-2-O-methyl-beta-L-fucopyranoside
C8 H16 O4 Se
JGCHFCAEXBTPJU-FMGWEMOISA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
I [auth A],
K [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
BO3
Query on BO3

Download Ideal Coordinates CCD File 
J [auth A]BORIC ACID
B H3 O3
KGBXLFKZBHKPEV-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth A],
L [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free:  0.167 (Depositor), 0.180 (DCC) 
  • R-Value Work:  0.133 (Depositor), 0.150 (DCC) 
  • R-Value Observed: 0.135 (Depositor) 
Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.058α = 90
b = 69.058β = 90
c = 349.211γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
SHELXphasing

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 6YRClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-29
    Type: Initial release
  • Version 1.1: 2018-02-14
    Changes: Database references
  • Version 1.2: 2018-03-14
    Changes: Database references
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Derived calculations, Other, Structure summary
  • Version 1.4: 2024-05-08
    Changes: Data collection, Database references, Structure summary