3UD9

Crystal Structure Analysis of FGF1-Disaccharide(NI23) complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.216 

wwPDB Validation 3D Report Full Report



Literature

Divergent synthesis of 48 heparan sulfate-based disaccharides and probing the specific sugar-fibroblast growth factor-1 interaction

Hu, Y.-P.Zhong, Y.-Q.Chen, Z.-G.Chen, C.-Y.Shi, Z.Zulueta, M.M.L.Ku, C.-C.Lee, P.-Y.Wang, C.-C.Hung, S.-C.

(2012) J Am Chem Soc 134: 20722-20727

  • DOI: 10.1021/ja3090065
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Several biological processes involve glycans, yet understanding their ligand specificities is impeded by their inherent diversity and difficult acquisition. Generating broad synthetic sugar libraries for bioevaluations is a powerful tool in unravelin ...

    Several biological processes involve glycans, yet understanding their ligand specificities is impeded by their inherent diversity and difficult acquisition. Generating broad synthetic sugar libraries for bioevaluations is a powerful tool in unraveling glycan structural information. In the case of the widely distributed heparan sulfate (HS), however, the 48 theoretical possibilities for its repeating disaccharide call for synthetic approaches that should minimize the effort in an undoubtedly huge undertaking. Here we employed a divergent strategy to afford all 48 HS-based disaccharides from just two orthogonally protected disaccharide precursors. Different combinations and sequence of transformation steps were applied with many downstream intermediates leading up to multiple target products. With the full disaccharide library in hand, affinity screening with fibroblast growth factor-1 (FGF-1) revealed that four of the synthetic sugars bind to FGF-1. The molecular details of the interaction were further clarified through X-ray analysis of the sugar-protein cocrystals. The capability of comprehensive sugar libraries in providing key insights in glycan-ligand interaction is, thus, highlighted.


    Organizational Affiliation

    Genomics Research Center, Academia Sinica, 128, Section 2, Academia Road, Taipei 115, Taiwan.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Heparin-binding growth factor 1A, B, C141Homo sapiensMutation(s): 0 
Gene Names: FGF1FGFA
Find proteins for P05230 (Homo sapiens)
Explore P05230 
Go to UniProtKB:  P05230
NIH Common Fund Data Resources
PHAROS  P05230
Protein Feature View
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  • Reference Sequence
Oligosaccharides
Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation
2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-1-O-methyl-2-O-sulfo-alpha-L-idopyranuronic acid
D
2 N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download CCD File 
A, C
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.216 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.574α = 90
b = 46.93β = 125.71
c = 96.708γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
EPMRphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2011-10-27 
  • Released Date: 2012-11-28 
  • Deposition Author(s): Hung, S.-C., Shi, Z.

Revision History 

  • Version 1.0: 2012-11-28
    Type: Initial release
  • Version 1.1: 2013-01-16
    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