1V7M

Human Thrombopoietin Functional Domain Complexed To Neutralizing Antibody TN1 Fab


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 0.316 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.232 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure of the receptor-binding domain of human thrombopoietin determined by complexation with a neutralizing antibody fragment

Feese, M.D.Tamada, T.Kato, Y.Maeda, Y.Hirose, M.Matsukura, Y.Shigematsu, H.Muto, T.Matsumoto, A.Watarai, H.Ogami, K.Tahara, T.Kato, T.Miyazaki, H.Kuroki, R.

(2004) Proc Natl Acad Sci U S A 101: 1816-1821

  • DOI: https://doi.org/10.1073/pnas.0308530100
  • Primary Citation of Related Structures:  
    1V7M, 1V7N

  • PubMed Abstract: 

    The cytokine thrombopoietin (TPO), the ligand for the hematopoietic receptor c-Mpl, acts as a primary regulator of megakaryocytopoiesis and platelet production. We have determined the crystal structure of the receptor-binding domain of human TPO (hTPO(163)) to a 2.5-A resolution by complexation with a neutralizing Fab fragment. The backbone structure of hTPO(163) has an antiparallel four-helix bundle fold. The neutralizing Fab mainly recognizes the C-D crossover loop containing the species invariant residue Q111. Titration calorimetric experiments show that hTPO(163) interacts with soluble c-Mpl containing the extracellular cytokine receptor homology domains with 1:2 stoichiometry with the binding constants of 3.3 x 10(9) M(-1) and 1.1 x 10(6) M(-1). The presence of the neutralizing Fab did not inhibit binding of hTPO(163) to soluble c-Mpl fragments, but the lower-affinity binding disappeared. Together with prior genetic data, these define the structure-function relationships in TPO and the activation scheme of c-Mpl.


  • Organizational Affiliation

    Central Laboratories for Key Technology, Kirin Brewery Co. Ltd., 1-13-5 Fukuura, Kanazawa-ku, Yokohama 236-0004, Japan.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Monoclonal TN1 Fab Light ChainA [auth L],
D [auth M]
213Mus musculusMutation(s): 0 
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Monoclonal TN1 Fab Heavy ChainB [auth H],
E [auth I]
217Mus musculusMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ThrombopoietinC [auth V],
F [auth X]
163Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P40225 (Homo sapiens)
Explore P40225 
Go to UniProtKB:  P40225
GTEx:  ENSG00000090534 
Entity Groups  
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UniProt GroupP40225
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 0.316 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.232 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 132.099α = 90
b = 46.771β = 90.48
c = 185.151γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-03-02
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-10-25
    Changes: Data collection, Database references, Refinement description