7NBI | pdb_00007nbi

Crystal structure of a monomeric FLT3 Ligand variant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 
    0.203 (Depositor), 0.203 (DCC) 
  • R-Value Work: 
    0.164 (Depositor), 0.165 (DCC) 
  • R-Value Observed: 
    0.166 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Engineering and crystal structure of a monomeric FLT3 ligand variant.

Pannecoucke, E.Raes, L.Savvides, S.N.

(2021) Acta Crystallogr F Struct Biol Commun 77: 121-127

  • DOI: https://doi.org/10.1107/S2053230X21003289
  • Primary Citation Related Structures: 
    7NBI

  • PubMed Abstract: 

    The overarching paradigm for the activation of class III and V receptor tyrosine kinases (RTKs) prescribes cytokine-mediated dimerization of the receptor ectodomains and homotypic receptor-receptor interactions. However, structural studies have shown that the hematopoietic receptor FLT3, a class III RTK, does not appear to engage in such receptor-receptor contacts, despite its efficient dimerization by dimeric FLT3 ligand (FL). As part of efforts to better understand the intricacies of FLT3 activation, we sought to engineer a monomeric FL. It was found that a Leu27Asp substitution at the dimer interface of the cytokine led to a stable monomeric cytokine (FL L27D ) without abrogation of receptor binding. The crystal structure of FL L27D at 1.65 Å resolution revealed that the introduced point mutation led to shielding of the hydrophobic footprint of the dimerization interface in wild-type FL without affecting the conformation of the FLT3 binding site. Thus, FL L27D can serve as a monomeric FL variant to further interrogate the assembly mechanism of extracellular complexes of FLT3 in physiology and disease.


  • Organizational Affiliation
    • Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Technologiepark-Zwijnaarde 71, 9052 Zwijnaarde, Belgium.

Macromolecule Content 

  • Total Structure Weight: 32.23 kDa 
  • Atom Count: 2,436 
  • Modeled Residue Count: 269 
  • Deposited Residue Count: 276 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Fms-related tyrosine kinase 3 ligand
A, B
138Homo sapiensMutation(s): 1 
Gene Names: FLT3LG
UniProt & NIH Common Fund Data Resources
Find proteins for P49771 (Homo sapiens)
Explore P49771 
Go to UniProtKB:  P49771
GTEx:  ENSG00000090554 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49771
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free:  0.203 (Depositor), 0.203 (DCC) 
  • R-Value Work:  0.164 (Depositor), 0.165 (DCC) 
  • R-Value Observed: 0.166 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 28.3α = 82.82
b = 43.49β = 85.41
c = 46.36γ = 85.1
Software Package:
Software NamePurpose
XDSdata scaling
PHASERphasing
PHENIXrefinement
BUSTERrefinement
XDSdata reduction

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Research Foundation - Flanders (FWO)Belgium--

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-28
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Database references, Refinement description
  • Version 1.2: 2024-11-13
    Changes: Structure summary