1CD9

2:2 COMPLEX OF G-CSF WITH ITS RECEPTOR

• PDB DOI: https://doi.org/10.2210/pdb1CD9/pdb

• Classification: CYTOKINE
• Organism(s): Homo sapiens, Mus musculus
• Expression System: Escherichia coli, Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 1999-03-08 Released: 2000-03-08 
• Deposition Author(s): Aritomi, M., Kunishima, N., Okamoto, T., Kuroki, R., Ota, Y., Morikawa, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.319 
• R-Value Work: 0.237 

Literature

Atomic structure of the GCSF-receptor complex showing a new cytokine-receptor recognition scheme.

Aritomi, M., Kunishima, N., Okamoto, T., Kuroki, R., Ota, Y., Morikawa, K.

(1999) Nature 401: 713-717

• PubMed: 10537111 
• DOI: https://doi.org/10.1038/44394
• Primary Citation of Related Structures:  
  1CD9, 1PGR


• PubMed Abstract: 
  

  Granulocyte colony-stimulating factor (GCSF) is the principal growth factor regulating the maturation, proliferation and differentiation of the precursor cells of neutrophilic granulocytes and is used to treat neutropenia. GCSF is a member of the long-chain subtype of the class 1 cytokine superfamily, which includes growth hormone, erythropoietin, interleukin 6 and oncostatin M. Here we have determined the crystal structure of GCSF complexed to the BN-BC domains, the principal ligand-binding region of the GCSF receptor (GCSFR). The two receptor domains form a complex in a 2:2 ratio with the ligand, with a non-crystallographic pseudo-twofold axis through primarily the interdomain region and secondarily the BC domain. This structural view of a gp130-type receptor-ligand complex presents a new molecular basis for cytokine-receptor recognition.

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Organizational Affiliation: 

Biomolecular Engineering Research Institute, Suita-city, Osaka, Japan.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 87 kDa 
• Atom Count: 6,080 
• Modelled Residue Count: 750 
• Deposited Residue Count: 780 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (GRANULOCYTE COLONY-STIMULATING FACTOR)	A, C	175	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P09919 (Homo sapiens) Explore P09919  Go to UniProtKB:  P09919
PHAROS:  P09919 GTEx:  ENSG00000108342

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (G-CSF RECEPTOR)	B, D	215	Mus musculus	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P40223 (Mus musculus) Explore P40223  Go to UniProtKB:  P40223
IMPC:  MGI:1339755

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	E [auth B], F [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.319 
• R-Value Work: 0.237 
• Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.467	α = 90
b = 125.467	β = 90
c = 372.771	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MLPHARE	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-03-08 
Deposition Author(s): Aritomi, M., Kunishima, N., Okamoto, T., Kuroki, R., Ota, Y., Morikawa, K.

Revision History  

• Version 1.0: 2000-03-08
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.4: 2023-12-27
  Changes: Data collection, Database references, Structure summary