1V7N

Human Thrombopoietin Functional Domain Complexed To Neutralizing Antibody TN1 Fab


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.167 

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, N, O
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, J, K
217N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Thrombopoietin
V, X, Y, Z
163Homo sapiensMutation(s): 1 
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: 3.3 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.167 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 133.038α = 90.00
b = 46.582β = 90.28
c = 191.359γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
AMoREphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



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