3QS7

Crystal structure of a human Flt3 ligand-receptor ternary complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.30 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.260 
  • R-Value Observed: 0.261 

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This is version 1.4 of the entry. See complete history. 


Literature

Structural insights into the extracellular assembly of the hematopoietic Flt3 signaling complex.

Verstraete, K., Vandriessche, G., Januar, M., Elegheert, J., Shkumatov, A.V., Desfosses, A., Van Craenenbroeck, K., Svergun, D.I., Gutsche, I., Vergauwen, B., Savvides, S.N.

(2011) Blood 118: 60-68

  • DOI: 10.1182/blood-2011-01-329532
  • Primary Citation of Related Structures:  
    3QS7, 3QS9

  • PubMed Abstract: 

    • The class III receptor tyrosine kinase (RTKIII) Fms-like tyrosine kinase receptor 3 (Flt3) and its cytokine ligand (FL) play central roles in hematopoiesis and the immune system, by establishing signaling cascades crucial for the development and homeostasis of hematopoietic progenitors and antigen-presenting dendritic cells ...

    The class III receptor tyrosine kinase (RTKIII) Fms-like tyrosine kinase receptor 3 (Flt3) and its cytokine ligand (FL) play central roles in hematopoiesis and the immune system, by establishing signaling cascades crucial for the development and homeostasis of hematopoietic progenitors and antigen-presenting dendritic cells. However, Flt3 is also one of the most frequently mutated receptors in hematologic malignancies and is currently a major prognostic factor and clinical target for acute myeloid leukemia. Here, we report the structural basis for the Flt3 ligand-receptor complex and unveil an unanticipated extracellular assembly unlike any other RTKIII/V complex characterized to date. FL induces dimerization of Flt3 via a remarkably compact binding epitope localized at the tip of extracellular domain 3 of Flt3, and it invokes a ternary complex devoid of homotypic receptor interactions. Comparisons of Flt3 with homologous receptors and available mutagenesis data for FL have allowed us to rationalize the unique features of the Flt3 extracellular assembly. Furthermore, thermodynamic dissection of complex formation points to a pronounced enthalpically driven binding event coupled to an entropic penalty. Together, our data suggest that the high-affinity Flt3:FL complex is driven in part by a single preformed binding epitope on FL reminiscent of a "lock-and-key" binding mode, thereby setting the stage for antagonist design.

    Related Citations: 
    • Inducible production of human Flt3 ectodomain variants in mammalian cells and preliminary crystallographic analysis of Flt3 ligand-receptor complexes
      Verstraete, K., Vandriessche, G., Januar, M., Elegheert, J., Shkumatov, A., Desfosses, A., Van Craenenbroeck, K., Svergun, D., Gutsche, I., Vergauwen, B., Savvides, S.N.
      () To be published --: --
    • Efficient production of bioactive recombinant human Flt3 ligand in E. coli.
      Verstraete, K., Koch, S., Ertugrul, S., Vandenberghe, I., Aerts, M., Vandriessche, G., Thiede, C., Savvides, S.N.
      (2009) Protein J 28: 57
    Organizational Affiliation: 

    Unit for Structural Biology, Laboratory for Protein Biochemistry and Biomolecular Engineering (L-ProBE), Ghent University, Ghent, Belgium.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SL cytokineA, B, C, D138Homo sapiensMutation(s): 0 
Gene Names: FLT3LG
UniProt & NIH Common Fund Data Resources
Find proteins for P49771 (Homo sapiens)
Explore P49771 
Go to UniProtKB:  P49771
PHAROS:  P49771
GTEx:  ENSG00000090554 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49771
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
FL cytokine receptorE, F, G, H423Homo sapiensMutation(s): 0 
Gene Names: FLT3, STK1, CD135, FLK2
EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P36888 (Homo sapiens)
Explore P36888 
Go to UniProtKB:  P36888
PHAROS:  P36888
GTEx:  ENSG00000122025 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP36888
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG
Download Ideal Coordinates CCD File 
I [auth E],
J [auth F],
K [auth F],
L [auth F],
M [auth G],
I [auth E],
J [auth F],
K [auth F],
L [auth F],
M [auth G],
N [auth H],
O [auth H]
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: 4.30 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.260 
  • R-Value Observed: 0.261 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.89α = 90
b = 146.26β = 109.66
c = 105.95γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
BUSTERrefinement

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-03-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-07-20
    Changes: Database references
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 1.4: 2021-03-31
    Changes: Source and taxonomy, Structure summary