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 

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.USA 101: 1816-1821

  • DOI: 10.1073/pnas.0308530100
  • Primary Citation of Related Structures:  

  • 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.,Sect.D 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Monoclonal TN1 Fab Light Chain
L, M
213N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Monoclonal TN1 Fab Heavy Chain
H, I
217N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Thrombopoietin
V, X
163Homo sapiensMutation(s): 0 
Gene Names: THPO (MGDF)
Find proteins for P40225 (Homo sapiens)
Go to Gene View: THPO
Go to UniProtKB:  P40225
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 0.316 
  • R-Value Work: 0.228 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 132.099α = 90.00
b = 46.771β = 90.48
c = 185.151γ = 90.00
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
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance