1F5F

CRYSTAL STRUCTURE OF THE N-TERMINAL G-DOMAIN OF SHBG IN COMPLEX WITH ZINC


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.197 

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This is version 1.3 of the entry. See complete history


Literature

Steroid-binding specificity of human sex hormone-binding globulin is influenced by occupancy of a zinc-binding site.

Avvakumov, G.V.Muller, Y.A.Hammond, G.L.

(2000) J Biol Chem 275: 25920-25925

  • DOI: https://doi.org/10.1074/jbc.M004484200
  • Primary Citation of Related Structures:  
    1F5F

  • PubMed Abstract: 

    One calcium-binding site (site I) and a second poorly defined metal-binding site (site II) have been observed previously within the amino-terminal laminin G-like domain (G domain) of human sex hormone-binding globulin (SHBG). By soaking crystals of this structure in 2.5 mm ZnCl(2), site II and a new metal-binding site (site III) were found to bind Zn(2+). Site II is located close to the steroid-binding site, and Zn(2+) is coordinated by the side chains of His(83) and His(136) and the carboxylate group of Asp(65). In this site, Zn(2+) prevents Asp(65) from interacting with the steroid 17beta-hydroxy group and alters the conformations of His(83) and His(136), as well as a disordered region over the steroid-binding site. Site III is formed by the side chains of His(101) and the carboxylate group of Asp(117), and the distance between them (2.7 A) is increased to 3.7 A in the presence of Zn(2+). The affinity of SHBG for estradiol is reduced in the presence of 0. 1-1 mm Zn(2+), whereas its affinity for androgens is unchanged, and chemically-related metal ions (Cd(2+) and Hg(2+)) have similar but less pronounced effects. This is not observed when Zn(2+) coordination at site II is modified by substituting Gln for His(136). An alteration in the steroid-binding specificity of human SHBG by Zn(2+) occupancy of site II may be relevant in male reproductive tissues where zinc concentrations are very high.


  • Organizational Affiliation

    Departments of Obstetrics & Gynecology and Pharmacology & Toxicology and Medical Research Council Group in Fetal and Neonatal Health and Development, University of Western Ontario, London, Ontario N6A 4L6, Canada.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SEX HORMONE-BINDING GLOBULIN205Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P04278 (Homo sapiens)
Explore P04278 
Go to UniProtKB:  P04278
PHAROS:  P04278
GTEx:  ENSG00000129214 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04278
Sequence Annotations
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  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
DHT BindingDB:  1F5F Kd: 0.18 (nM) from 1 assay(s)
IC50: 3.8 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.197 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.02α = 90
b = 104.02β = 90
c = 84.71γ = 120
Software Package:
Software NamePurpose
XDSdata scaling
XDSdata reduction
REFMACrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-09-06
    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: 2018-04-04
    Changes: Data collection