5D3I

Crystal structure of the SSL3-TLR2 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.233 

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Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

Structural basis for inhibition of TLR2 by staphylococcal superantigen-like protein 3 (SSL3).

Koymans, K.J.Feitsma, L.J.Brondijk, T.H.Aerts, P.C.Lukkien, E.Lossl, P.van Kessel, K.P.de Haas, C.J.van Strijp, J.A.Huizinga, E.G.

(2015) Proc Natl Acad Sci U S A 112: 11018-11023

  • DOI: https://doi.org/10.1073/pnas.1502026112
  • Primary Citation of Related Structures:  
    5D3D, 5D3I

  • PubMed Abstract: 

    Toll-like receptors (TLRs) are crucial in innate recognition of invading micro-organisms and their subsequent clearance. Bacteria are not passive bystanders and have evolved complex evasion mechanisms. Staphylococcus aureus secretes a potent TLR2 antagonist, staphylococcal superantigen-like protein 3 (SSL3), which prevents receptor stimulation by pathogen-associated lipopeptides. Here, we present crystal structures of SSL3 and its complex with TLR2. The structure reveals that formation of the specific inhibitory complex is predominantly mediated by hydrophobic contacts between SSL3 and TLR2 and does not involve interaction of TLR2-glycans with the conserved Lewis(X) binding site of SSL3. In the complex, SSL3 partially covers the entrance to the lipopeptide binding pocket in TLR2, reducing its size by ∼50%. We show that this is sufficient to inhibit binding of agonist Pam2CSK4 effectively, yet allows SSL3 to bind to an already formed TLR2-Pam2CSK4 complex. The binding site of SSL3 overlaps those of TLR2 dimerization partners TLR1 and TLR6 extensively. Combined, our data reveal a robust dual mechanism in which SSL3 interferes with TLR2 activation at two stages: by binding to TLR2, it blocks ligand binding and thus inhibits activation. Second, by interacting with an already formed TLR2-lipopeptide complex, it prevents TLR heterodimerization and downstream signaling.


  • Organizational Affiliation

    Department of Medical Microbiology, University Medical Center Utrecht, NL-3584 CX, Utrecht, The Netherlands;


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Toll-like receptor 2568Mus musculusMutation(s): 0 
Gene Names: Tlr2
UniProt
Find proteins for Q9QUN7 (Mus musculus)
Explore Q9QUN7 
Go to UniProtKB:  Q9QUN7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9QUN7
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Staphylococcal Superantigen-Like protein 3195Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: SAOUHSC_00386
UniProt
Find proteins for Q2G0X7 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Explore Q2G0X7 
Go to UniProtKB:  Q2G0X7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2G0X7
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PCW
Query on PCW

Download Ideal Coordinates CCD File 
E [auth A]1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H85 N O8 P
SNKAWJBJQDLSFF-NVKMUCNASA-O
NAG
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
CL
Query on CL

Download Ideal Coordinates CCD File 
F [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.233 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.198α = 90
b = 104.198β = 90
c = 153.625γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Netherlands Organization for Scientific ResearchNetherlandsECHO Grant 700.58.006
Netherlands Organization for Health Research and DevelopmentNetherlandsZonMw Grant 205200004
Dutch Top Institute Pharma ProjectNetherlandsD1-101

Revision History  (Full details and data files)

  • Version 1.0: 2015-08-19
    Type: Initial release
  • Version 1.1: 2015-09-02
    Changes: Database references
  • Version 1.2: 2015-09-09
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary