8QUP | pdb_00008qup

G-CSFR inhibitor Bop1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 
    0.265 (Depositor), 0.267 (DCC) 
  • R-Value Work: 
    0.226 (Depositor), 0.232 (DCC) 
  • R-Value Observed: 
    0.228 (Depositor) 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A strategy to design protein-based antagonists against type I cytokine receptors.

Ullrich, T.Klimenkova, O.Pollmann, C.Lasram, A.Hatskovska, V.Maksymenko, K.Milijas-Jotic, M.Schenk, L.Lengerke, C.Hartmann, M.D.Piehler, J.Skokowa, J.ElGamacy, M.

(2024) PLoS Biol 22: e3002883-e3002883

  • DOI: https://doi.org/10.1371/journal.pbio.3002883
  • Primary Citation of Related Structures:  
    8QUP

  • PubMed Abstract: 

    Excessive cytokine signaling resulting from dysregulation of a cytokine or its receptor can be a main driver of cancer, autoimmune, or hematopoietic disorders. Here, we leverage protein design to create tailored cytokine receptor blockers with idealized properties. Specifically, we aimed to tackle the granulocyte-colony stimulating factor receptor (G-CSFR), a mediator of different types of leukemia and autoinflammatory diseases. By modifying designed G-CSFR binders, we engineered hyper-stable proteins that function as nanomolar signaling antagonists. X-ray crystallography showed atomic-level agreement with the experimental structure of an exemplary design. Furthermore, the most potent design blocks G-CSFR in acute myeloid leukemia cells and primary human hematopoietic stem cells. Thus, the resulting designs can be used for inhibiting or homing to G-CSFR-expressing cells. Our results also demonstrate that similarly designed cytokine mimics can be used to derive antagonists to tackle other type I cytokine receptors.


  • Organizational Affiliation
    • Max Planck Institute for Biology, Department of Protein Evolution, Tübingen, Germany.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bop1124synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free:  0.265 (Depositor), 0.267 (DCC) 
  • R-Value Work:  0.226 (Depositor), 0.232 (DCC) 
  • R-Value Observed: 0.228 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 23.262α = 93.02
b = 29.132β = 92.6
c = 37.76γ = 97.87
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Max Planck SocietyGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-23
    Type: Initial release
  • Version 1.1: 2025-12-10
    Changes: Database references
  • Version 1.2: 2025-12-24
    Changes: Structure summary