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), 0.179 (DCC) 
  • R-Value Work: 
    0.133 (Depositor), 0.151 (DCC) 
  • R-Value Observed: 
    0.135 (Depositor) 

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Ligand Structure Quality Assessment 


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 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.

Macromolecule Content 

  • Total Structure Weight: 50.74 kDa 
  • Atom Count: 4,081 
  • Modeled Residue Count: 449 
  • Deposited Residue Count: 454 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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
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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]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
M [auth B],
N [auth B],
O [auth B],
P [auth B],
Q [auth B],
R [auth B]
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), 0.179 (DCC) 
  • R-Value Work:  0.133 (Depositor), 0.151 (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

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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