Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 53.82 kDa 
• Atom Count: 3647 
• Modelled Residue Count: 467 
• Deposited Residue Count: 487 
• Unique protein chains: 2

2D9Q

Crystal Structure of the Human GCSF-Receptor Signaling Complex

• DOI: 10.2210/pdb2D9Q/pdb

• Classification: SIGNALING PROTEIN/CYTOKINE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli, Spodoptera frugiperda
• Mutation(s): Yes 


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

---

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 

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

• PubMed: 16492764 
• 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. 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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CSF3	A	174	Homo sapiens	Mutation(s): 0  Gene Names: CSF3, C17orf33, GCSF
Find proteins for P09919 (Homo sapiens) Explore P09919  Go to UniProtKB:  P09919
NIH Common Fund Data Resources
PHAROS:  P09919 GTEx:  ENSG00000108342

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Granulocyte colony-stimulating factor receptor	B	313	Homo sapiens	Mutation(s): 3  Gene Names: CSF3R, GCSFR
Find proteins for Q99062 (Homo sapiens) Explore Q99062  Go to UniProtKB:  Q99062
NIH Common Fund Data Resources
PHAROS:  Q99062 GTEx:  ENSG00000119535

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	2		N-Glycosylation

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 = 134.777	α = 90
b = 134.777	β = 90
c = 105.468	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MLPHARE	phasing
SHARP	phasing
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• 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