1IMX

1.8 Angstrom crystal structure of IGF-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 
    0.258 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.245 (Depositor), 0.240 (DCC) 

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Ligand Structure Quality Assessment 

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This is version 1.3 of the entry. See complete history


Literature

Crystal structure of human insulin-like growth factor-1: detergent binding inhibits binding protein interactions.

Vajdos, F.F.Ultsch, M.Schaffer, M.L.Deshayes, K.D.Liu, J.Skelton, N.J.de Vos, A.M.

(2001) Biochemistry 40: 11022-11029

  • DOI: https://doi.org/10.1021/bi0109111
  • Primary Citation of Related Structures:  
    1IMX

  • PubMed Abstract: 

    Despite efforts spanning considerably more than a decade, a high-resolution view of the family of proteins known as insulin-like growth factors (IGFs) has remained elusive. IGF-1 consists of three helical segments which are connected by a 12-residue linker known as the C-region. NMR studies of members of this family reveal a dynamic structure with a topology resembling insulin but little structural definition in the C-region. We have crystallized IGF-1 in the presence of the detergent deoxy big CHAPS, and determined its structure at 1.8 A resolution by multiwavelength anomalous diffraction, exploiting the anomalous scattering of a single bromide ion and six of the seven sulfur atoms of IGF-1. The structure reveals a well-defined conformation for much of the C-region, which extends away from the core of IGF-1 and has residues known to be involved in receptor binding prominently displayed in a type II beta-turn. In the crystal, these residues form a dimer interface, but analytical ultracentrifugation experiments demonstrate that at physiological concentrations IGF-1 is monomeric. A single detergent molecule contacts residues known to be important for IGF-1 binding protein (IGFBP) interactions. Biophysical and biochemical data show that the detergent binds to IGF-1 specifically and blocks binding of IGFBP-1 and IGFBP-3.


  • Organizational Affiliation

    Department of Protein Engineering, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Insulin-like Growth Factor 1A70Homo sapiensMutation(s): 0 
Gene Names: IGF-1
UniProt & NIH Common Fund Data Resources
Find proteins for P05019 (Homo sapiens)
Explore P05019 
Go to UniProtKB:  P05019
PHAROS:  P05019
GTEx:  ENSG00000017427 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05019
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free:  0.258 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.245 (Depositor), 0.240 (DCC) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 31.831α = 90
b = 71.055β = 90
c = 65.996γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
CNXrefinement

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted CPQClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-09-05
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-11-20
    Changes: Data collection, Database references, Derived calculations, Structure summary