4B9H

Cladosporium fulvum LysM effector Ecp6 in complex with a beta-1,4- linked N-acetyl-D-glucosamine tetramer: I3C heavy atom derivative


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.213 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

Fungal Effector Ecp6 Outcompetes Host Immune Receptor for Chitin Binding Through Intrachain Lysm Dimerization

Sanchez-Vallet, A.Saleem-Batcha, R.Kombrink, A.Hansen, G.Valkenburg, D.J.Thomma, B.P.H.J.Mesters, J.R.

(2013) Elife 2: 00790

  • DOI: 10.7554/eLife.00790
  • Primary Citation of Related Structures:  
    4B8V, 4B9H

  • PubMed Abstract: 
  • While host immune receptors detect pathogen-associated molecular patterns to activate immunity, pathogens attempt to deregulate host immunity through secreted effectors. Fungi employ LysM effectors to prevent recognition of cell wall-derived chitin by host immune receptors, although the mechanism to compete for chitin binding remained unclear ...

    While host immune receptors detect pathogen-associated molecular patterns to activate immunity, pathogens attempt to deregulate host immunity through secreted effectors. Fungi employ LysM effectors to prevent recognition of cell wall-derived chitin by host immune receptors, although the mechanism to compete for chitin binding remained unclear. Structural analysis of the LysM effector Ecp6 of the fungal tomato pathogen Cladosporium fulvum reveals a novel mechanism for chitin binding, mediated by intrachain LysM dimerization, leading to a chitin-binding groove that is deeply buried in the effector protein. This composite binding site involves two of the three LysMs of Ecp6 and mediates chitin binding with ultra-high (pM) affinity. Intriguingly, the remaining singular LysM domain of Ecp6 binds chitin with low micromolar affinity but can nevertheless still perturb chitin-triggered immunity. Conceivably, the perturbation by this LysM domain is not established through chitin sequestration but possibly through interference with the host immune receptor complex. DOI:http://dx.doi.org/10.7554/eLife.00790.001.


    Related Citations: 
    • Conserved Fungal Lysm Effector Ecp6 Prevents Chitin-Triggered Immunity in Plants.
      De Jonge, R., Van Esse, H.P., Kombrink, A., Shinya, T., Desaki, Y., Bours, R., Van Der Krol, S., Shibuya, N., Joosten, M.H.A.J., Thomma, B.P.H.J.
      (2010) Science 329: 953

    Organizational Affiliation

    Centro de Biotecnología y Genómica de Plantas , Universidad Politécnica de Madrid , Madrid , Spain ; Laboratory of Phytopathology , Wageningen University , Wageningen , Netherlands.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
EXTRACELLULAR PROTEIN 6A228Passalora fulvaMutation(s): 0 
UniProt
Find proteins for B3VBK9 (Passalora fulva)
Explore B3VBK9 
Go to UniProtKB:  B3VBK9
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-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseB2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranoseC4N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G93613RO
GlyCosmos:  G93613RO
GlyGen:  G93613RO
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
I3C (Subject of Investigation/LOI)
Query on I3C

Download Ideal Coordinates CCD File 
E [auth A]5-amino-2,4,6-triiodobenzene-1,3-dicarboxylic acid
C8 H4 I3 N O4
JEZJSNULLBSYHV-UHFFFAOYSA-N
 Ligand Interaction
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
D [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.213 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.889α = 90
b = 57.889β = 90
c = 119.679γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-07-17
    Type: Initial release
  • Version 1.1: 2013-09-25
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary