1V7N

Human Thrombopoietin Functional Domain Complexed To Neutralizing Antibody TN1 Fab


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.174 

wwPDB Validation   3D Report Full Report


This is version 1.2 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: 10.1073/pnas.0308530100
  • Primary Citation of Related Structures:  
    1V7N, 1V7M

  • 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 (hTP ...

    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.


    Related Citations: 
    • Crystallization of the Functional Domain of Human Thrombopoietin Using an Antigen-Binding Fragment Derived from Neutralizing Monoclonal Antibody
      Kuroki, R., Hirose, M., Kato, Y., Feese, M.D., Tamada, T., Shigematsu, H., Watarai, H., Maeda, Y., Tahara, T., Kato, T., Miyazaki, H.
      (2002) Acta Crystallogr D Biol Crystallogr 58: 856

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Monoclonal TN1 Fab Light ChainLMNO213Mus musculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Monoclonal TN1 Fab Heavy ChainHIJK217Mus musculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
ThrombopoietinVXYZ163Homo sapiensMutation(s): 1 
Gene Names: THPOMGDF
Find proteins for P40225 (Homo sapiens)
Explore P40225 
Go to UniProtKB:  P40225
NIH Common Fund Data Resources
PHAROS  P40225
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.174 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 133.038α = 90
b = 46.582β = 90.28
c = 191.359γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • 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