2PF5

Crystal Structure of the Human TSG-6 Link Module


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Plasticity of the TSG-6 HA-binding loop and mobility in the TSG-6-HA complex revealed by NMR and X-ray crystallography

Higman, V.A.Blundell, C.D.Mahoney, D.J.Redfield, C.Noble, M.E.Day, A.J.

(2007) J Mol Biol 371: 669-684

  • DOI: 10.1016/j.jmb.2007.05.073
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Tumour necrosis factor-stimulated gene-6 (TSG-6) is a glycosaminoglycan-binding protein expressed during inflammatory and inflammation-like processes. Previously NMR structures were calculated for the Link module of TSG-6 (Link_TSG6) in its free stat ...

    Tumour necrosis factor-stimulated gene-6 (TSG-6) is a glycosaminoglycan-binding protein expressed during inflammatory and inflammation-like processes. Previously NMR structures were calculated for the Link module of TSG-6 (Link_TSG6) in its free state and when bound to an octasaccharide of hyaluronan (HA(8)). Heparin was found to compete for HA binding even though it interacts at a site that is distinct from the HA-binding surface. Here we present crystallography data on the free protein, and (15)N NMR relaxation data for the uncomplexed and HA(8)-bound forms of Link_TSG6. Although the Link module is comparatively rigid overall, the free protein shows a high degree of mobility in the beta4/beta5 loop and at the Cys47-Cys68 disulfide bond, both of which are regions involved in HA binding. When bound to HA(8), this dynamic behaviour is dampened, but not eliminated, suggesting a degree of dynamic matching between the protein and sugar that may decrease the entropic penalty of complex formation. A further highly dynamic residue is Lys54, which is distant from the HA-binding site, but was previously shown to be involved in heparin binding. When HA is bound, Lys54 becomes less mobile, providing evidence for an allosteric effect linking the HA and heparin-binding sites. A mechanism is suggested involving the beta2-strand and alpha2-helix. The crystal structure of free Link_TSG6 contains five molecules in the asymmetric unit that are highly similar to the NMR structure and support the dynamic behaviour seen near the HA-binding site: they show little or no electron density for the beta4/beta5 loop and display multiple conformations for the Cys47-Cys68 disulfide bond. The crystal structures were used in docking calculations with heparin. An extended interface between a Link_TSG6 dimer and heparin 11-mer was identified that is in excellent agreement with previous mutagenesis and calorimetric data, providing the basis for further investigation of this interaction.


    Organizational Affiliation

    MRC Immunochemistry Unit, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tumor necrosis factor-inducible protein TSG-6
A, B, C, D, E
98Homo sapiensMutation(s): 0 
Gene Names: TNFAIP6TSG6
Find proteins for P98066 (Homo sapiens)
Go to UniProtKB:  P98066
NIH Common Fund Data Resources
PHAROS  P98066
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2PE
Query on 2PE

Download CCD File 
B, D, E
NONAETHYLENE GLYCOL
C18 H38 O10
YZUUTMGDONTGTN-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
B, E
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 134.816α = 90
b = 75.87β = 103.42
c = 90.674γ = 90
Software Package:
Software NamePurpose
DNAdata collection
DMmodel building
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
DMphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-06-26
    Type: Initial release
  • Version 1.1: 2007-11-19
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance