2D9Q

Crystal Structure of the Human GCSF-Receptor Signaling Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.253 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Homodimeric cross-over structure of the human granulocyte colony-stimulating factor (GCSF) receptor signaling complex

Tamada, T.Honjo, E.Maeda, Y.Okamoto, T.Ishibashi, M.Tokunaga, M.Kuroki, R.

(2006) Proc Natl Acad Sci U S A 103: 3135-3140

  • DOI: 10.1073/pnas.0511264103
  • Primary Citation of Related Structures:  
    2D9Q

  • PubMed Abstract: 
  • A crystal structure of the signaling complex between human granulocyte colony-stimulating factor (GCSF) and a ligand binding region of GCSF receptor (GCSF-R), has been determined to 2.8 A resolution. The GCSF:GCSF-R complex formed a 2:2 stoichiometry by means of a cross-over interaction between the Ig-like domains of GCSF-R and GCSF ...

    A crystal structure of the signaling complex between human granulocyte colony-stimulating factor (GCSF) and a ligand binding region of GCSF receptor (GCSF-R), has been determined to 2.8 A resolution. The GCSF:GCSF-R complex formed a 2:2 stoichiometry by means of a cross-over interaction between the Ig-like domains of GCSF-R and GCSF. The conformation of the complex is quite different from that between human GCSF and the cytokine receptor homologous domain of mouse GCSF-R, but similar to that of the IL-6/gp130 signaling complex. The Ig-like domain cross-over structure necessary for GCSF-R activation is consistent with previously reported thermodynamic and mutational analyses.


    Related Citations: 
    • Crystallization of a 2:2 complex of granulocyte-colony stimulating factor (GCSF) with the ligand-binding region of the GCSF receptor
      Honjo, E., Tamada, T., Meada, Y., Koshiba, T., Matsukura, Y., Okamoto, T., Ishibashi, M., Tokunaga, M., Kuroki, R.
      (2005) Acta Crystallogr Sect F Struct Biol Cryst Commun 61: 788
    • Thermodynamic analysis of the activation mechanism of the GCSF receptor induced by ligand binding
      Mine, S., Koshiba, T., Honjo, E., Okamoto, T., Tamada, T., Maeda, Y., Matsukura, Y., Horie, A., Ishibashi, M., Sato, M., Azuma, M., Tokunaga, M., Nitta, K., Kuroki, R.
      (2004) Biochemistry 43: 2458

    Organizational Affiliation

    Research Group for Molecular Structural Biology, Quantum Beam Science Directorate, Japan Atomic Energy Agency, Tokai, Ibaraki.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CSF3A174Homo sapiensMutation(s): 0 
Gene Names: CSF3C17orf33GCSF
Find proteins for P09919 (Homo sapiens)
Explore P09919 
Go to UniProtKB:  P09919
NIH Common Fund Data Resources
PHAROS:  P09919
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Granulocyte colony-stimulating factor receptorB313Homo sapiensMutation(s): 3 
Gene Names: CSF3RGCSFR
Find proteins for Q99062 (Homo sapiens)
Explore Q99062 
Go to UniProtKB:  Q99062
NIH Common Fund Data Resources
PHAROS:  Q99062
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseC2 N-Glycosylation Oligosaccharides Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.253 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 134.777α = 90
b = 134.777β = 90
c = 105.468γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MLPHAREphasing
SHARPphasing
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2005-12-12 
  • Released Date: 2006-02-07 
  • Deposition Author(s): Tamada, T., Kuroki, R.

Revision History  (Full details and data files)

  • Version 1.0: 2006-02-07
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary