1D2S

CRYSTAL STRUCTURE OF THE N-TERMINAL LAMININ G-LIKE DOMAIN OF SHBG IN COMPLEX WITH DIHYDROTESTOSTERONE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

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: 504-512

  • DOI: 10.1093/emboj/19.4.504

  • PubMed Abstract: 
  • Human sex hormone-binding globulin (SHBG) transports sex steroids in blood and regulates their access to target tissues. In biological fluids, SHBG exists as a homodimer and each monomer comprises two laminin G-like domains (G domains). The crystal s ...

    Human sex hormone-binding globulin (SHBG) transports sex steroids in blood and regulates their access to target tissues. In biological fluids, SHBG exists as a homodimer and each monomer comprises two laminin G-like domains (G domains). The crystal structure of the N-terminal G domain of SHBG in complex with 5alpha-dihydrotestosterone at 1.55 A resolution reveals both the architecture of the steroid-binding site and the quaternary structure of the dimer. We also show that G domains have jellyroll topology and are structurally related to pentraxin. In each SHBG monomer, the steroid intercalates into a hydrophobic pocket within the beta-sheet sandwich. The steroid and a 20 A distant calcium ion are not located at the dimer interface. Instead, two separate steroid-binding pockets and calcium-binding sites exist per dimer. The structure displays intriguing disorder for loop segment Pro130-Arg135. In all other jellyroll proteins, this loop is well ordered. If modelled accordingly, it covers the steroid-binding site and could thereby regulate access of ligands to the binding pocket.


    Organizational Affiliation

    Forschungsgruppe Kristallographie, Max-Delbrück-Center for Molecular Medicine, Robert-Roessle-Strasse 10, D-13092 Berlin, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SEX HORMONE-BINDING GLOBULIN
A
170Homo sapiensMutation(s): 0 
Gene Names: SHBG
Find proteins for P04278 (Homo sapiens)
Go to Gene View: SHBG
Go to UniProtKB:  P04278
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
DHT
Query on DHT

Download SDF File 
Download CCD File 
A
5-ALPHA-DIHYDROTESTOSTERONE
C19 H30 O2
NVKAWKQGWWIWPM-ABEVXSGRSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DHTIC50: 3.8 nM (96) BINDINGDB
DHTKd: 0.2 nM (96) BINDINGDB
DHTKd: 0.182 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.205 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 104.040α = 90.00
b = 104.040β = 90.00
c = 84.430γ = 120.00
Software Package:
Software NamePurpose
MAR345data collection
MLPHAREphasing
XDSdata reduction
XDSdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-06-28
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description
  • Version 1.4: 2018-01-31
    Type: Experimental preparation