5GW9 | pdb_00005gw9

Crystal structure of C163, a backbone circularized G-CSF


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 
    0.218 (Depositor), 0.228 (DCC) 
  • R-Value Work: 
    0.177 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.179 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history

Literature

Structural insights into the backbone-circularized granulocyte colony-stimulating factor containing a short connector.

Miyafusa, T.Shibuya, R.Honda, S.

(2018) Biochem Biophys Res Commun 500: 224-228

  • DOI: https://doi.org/10.1016/j.bbrc.2018.04.045
  • Primary Citation Related Structures: 
    5GW9

  • PubMed Abstract: 

    Backbone circularization is a powerful approach for enhancing the structural stability of polypeptides. Herein, we present the crystal structure of the circularized variant of the granulocyte colony-stimulating factor (G-CSF) in which the terminal helical region was circularized using a short, two-amino acid connector. The structure revealed that the N- and C-termini were indeed connected by a peptide bond. The local structure of the C-terminal region transited from an α helix to 3 10 helix with a bend close to the N-terminal region, indicating that the structural change offset the insufficient length of the connector. This is the first-ever report of a crystal structure of the backbone of a circularized protein. It will facilitate the development of backbone circularization methodology.


  • Organizational Affiliation
    • Biomedical Research Institute, The National Institute of Advanced Industrial Science and Technology, Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan.

Macromolecule Content 

  • Total Structure Weight: 70.39 kDa 
  • Atom Count: 5,803 
  • Modeled Residue Count: 652 
  • Deposited Residue Count: 652 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Granulocyte colony-stimulating factor
A, B, C, D
163Homo sapiensMutation(s): 3 
Gene Names: CSF3C17orf33GCSF
UniProt & NIH Common Fund Data Resources
Find proteins for P09919 (Homo sapiens)
Explore P09919 
Go to UniProtKB:  P09919
PHAROS:  P09919
GTEx:  ENSG00000108342 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09919
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free:  0.218 (Depositor), 0.228 (DCC) 
  • R-Value Work:  0.177 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.179 (Depositor) 
Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.941α = 90
b = 60.941β = 90
c = 178.509γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of ScienceJapan23510273

Revision History  (Full details and data files)

  • Version 1.0: 2017-09-13
    Type: Initial release
  • Version 1.1: 2018-04-25
    Changes: Data collection, Database references
  • Version 1.2: 2018-05-16
    Changes: Data collection, Database references
  • Version 1.3: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2024-10-30
    Changes: Structure summary