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 

wwPDB Validation 3D Report Full Report


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: 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 t ...

    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.


    Related Citations: 
    • Crystal Structure of Human Sex Hormone-Binding Globulin: Steroid Transport by a Laminin G-Like Domain
      Grishkovskaya, I., Avvakumov, G.V., Sklenar, G., Dales, D., Hammond, G.L., Muller, Y.A.
      (2000) EMBO J 19: 504

    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
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SEX HORMONE-BINDING GLOBULINA205Homo sapiensMutation(s): 0 
Gene Names: SHBG
Find proteins for P04278 (Homo sapiens)
Explore P04278 
Go to UniProtKB:  P04278
NIH Common Fund Data Resources
PHAROS  P04278
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DHT
Query on DHT

Download CCD File 
A
5-ALPHA-DIHYDROTESTOSTERONE
C19 H30 O2
NVKAWKQGWWIWPM-ABEVXSGRSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
IPA
Query on IPA

Download CCD File 
A
ISOPROPYL ALCOHOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DHTIC50:  3.799999952316284   nM  BindingDB
DHTKd:  0.18000000715255737   nM  BindingDB
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

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • 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