4OEG

Crystal Structure Analysis of FGF2-Disaccharide (S9I2) complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.175 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Interactions that influence the binding of synthetic heparan sulfate based disaccharides to fibroblast growth factor-2.

Li, Y.C.Ho, I.H.Ku, C.C.Zhong, Y.Q.Hu, Y.P.Chen, Z.G.Chen, C.Y.Lin, W.C.Zulueta, M.M.Hung, S.C.Lin, M.G.Wang, C.C.Hsiao, C.D.

(2014) ACS Chem Biol 9: 1712-1717

  • DOI: 10.1021/cb500298q
  • Primary Citation of Related Structures:  
    4OEE, 4OEF, 4OEG

  • PubMed Abstract: 
  • Heparan sulfate (HS) is a linear sulfated polysaccharide that mediates protein activities at the cell-extracellular interface. Its interactions with proteins depend on the complex patterns of sulfonations and sugar residues. Previously, we synthesized all 48 potential disaccharides found in HS and used them for affinity screening and X-ray structural analysis with fibroblast growth factor-1 (FGF1) ...

    Heparan sulfate (HS) is a linear sulfated polysaccharide that mediates protein activities at the cell-extracellular interface. Its interactions with proteins depend on the complex patterns of sulfonations and sugar residues. Previously, we synthesized all 48 potential disaccharides found in HS and used them for affinity screening and X-ray structural analysis with fibroblast growth factor-1 (FGF1). Herein, we evaluated the affinities of the same sugars against FGF2 and determined the crystal structures of FGF2 in complex with three disaccharides carrying N-sulfonated glucosamine and 2-O-sulfonated iduronic acid as basic backbones. The crystal structures show that water molecules mediate different interactions between the 3-O-sulfonate group and Lys125. Moreover, the 6-O-sulfonate group forms intermolecular interactions with another FGF2 unit apart from the main binding site. These findings suggest that the water-mediated interactions and the intermolecular interactions influence the binding affinity of different disaccharides with FGF2, correlating with their respective dissociation constants in solution.


    Organizational Affiliation

    Institute of Molecular Biology, ‡Genomics Research Center, and §Institute of Chemistry, Academia Sinica , Taipei 115, Taiwan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Fibroblast growth factor 2A155Homo sapiensMutation(s): 2 
Gene Names: FGF2FGFB
UniProt & NIH Common Fund Data Resources
Find proteins for P09038 (Homo sapiens)
Explore P09038 
Go to UniProtKB:  P09038
PHAROS:  P09038
Protein Feature View
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-deoxy-3,6-di-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-1-O-methyl-2-O-sulfo-alpha-L-idopyranuronic acidB2N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G30346PQ
GlyCosmos:  G30346PQ
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.175 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 30.422α = 65.53
b = 32.994β = 71.79
c = 35.607γ = 77
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

  • Deposited Date: 2014-01-13 
  • Released Date: 2014-07-09 
  • Deposition Author(s): Li, Y.C., Hsiao, C.D.

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-09-10
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary