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 1V7N | pdb_00001v7n

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 (Depositor), 0.294 (DCC) 
  • R-Value Work: 
    0.167 (Depositor), 0.162 (DCC) 
  • R-Value Observed: 
    0.174 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 1V7N

This is version 1.5 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 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.

Macromolecule Content 

  • Total Structure Weight: 256.85 kDa 
  • Atom Count: 17,466 
  • Modeled Residue Count: 2,278 
  • Deposited Residue Count: 2,372 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Monoclonal TN1 Fab Light ChainA [auth L],
C [auth M],
E [auth N],
G [auth O]
213Mus musculusMutation(s): 0 
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Monoclonal TN1 Fab Heavy ChainB [auth H],
D [auth I],
F [auth J],
H [auth K]
217Mus musculusMutation(s): 0 
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
ThrombopoietinI [auth V],
J [auth X],
K [auth Y],
L [auth Z]
163Homo sapiensMutation(s): 1 
UniProt & NIH Common Fund Data Resources
Find proteins for P40225 (Homo sapiens)
Explore P40225 
Go to UniProtKB:  P40225
PHAROS:  P40225
GTEx:  ENSG00000090534 
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UniProt GroupP40225
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free:  0.305 (Depositor), 0.294 (DCC) 
  • R-Value Work:  0.167 (Depositor), 0.162 (DCC) 
  • R-Value Observed: 0.174 (Depositor) 
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  (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: 2021-11-10
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-10-25
    Changes: Data collection, Refinement description
  • Version 1.5: 2024-10-09
    Changes: Structure summary