3L3X | pdb_00003l3x

Crystal structure of DHT-bound androgen receptor in complex with the first motif of steroid receptor coactivator 3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 
    0.206 (Depositor), 0.211 (DCC) 
  • R-Value Work: 
    0.179 (Depositor), 0.191 (DCC) 
  • R-Value Observed: 
    0.181 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Identification of SRC3/AIB1 as a Preferred Coactivator for Hormone-activated Androgen Receptor.

Zhou, X.E.Suino-Powell, K.M.Li, J.He, Y.Mackeigan, J.P.Melcher, K.Yong, E.L.Xu, H.E.

(2010) J Biological Chem 285: 9161-9171

  • DOI: https://doi.org/10.1074/jbc.M109.085779
  • Primary Citation Related Structures: 
    3L3X, 3L3Z

  • PubMed Abstract: 

    Transcription activation by androgen receptor (AR), which depends on recruitment of coactivators, is required for the initiation and progression of prostate cancer, yet the mechanisms of how hormone-activated AR interacts with coactivators remain unclear. This is because AR, unlike any other nuclear receptor, prefers its own N-terminal FXXLF motif to the canonical LXXLL motifs of coactivators. Through biochemical and crystallographic studies, we identify that steroid receptor coactivator-3 (SRC3) (also named as amplified in breast cancer-1 or AIB1) interacts strongly with AR via synergistic binding of its first and third LXXLL motifs. Mutagenesis and functional studies confirm that SRC3 is a preferred coactivator for hormone-activated AR. Importantly, AR mutations found in prostate cancer patients correlate with their binding potency to SRC3, corroborating with the emerging role of SRC3 as a prostate cancer oncogene. These results provide a molecular mechanism for the selective utilization of SRC3 by hormone-activated AR, and they link the functional relationship between AR and SRC3 to the development and growth of prostate cancer.


  • Organizational Affiliation
    • Laboratory of Structural Sciences, Van Andel Research Institute, Grand Rapids, Michigan 49503, USA.

Macromolecule Content 

  • Total Structure Weight: 30.8 kDa 
  • Atom Count: 2,369 
  • Modeled Residue Count: 262 
  • Deposited Residue Count: 262 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Androgen receptor250Homo sapiensMutation(s): 0 
Gene Names: ARDHTRNR3C4
UniProt & NIH Common Fund Data Resources
Find proteins for P10275 (Homo sapiens)
Explore P10275 
Go to UniProtKB:  P10275
PHAROS:  P10275
GTEx:  ENSG00000169083 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10275
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Nuclear receptor coactivator 312Homo sapiensMutation(s): 0 
EC: 2.3.1.48
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y6Q9 (Homo sapiens)
Explore Q9Y6Q9 
Go to UniProtKB:  Q9Y6Q9
PHAROS:  Q9Y6Q9
GTEx:  ENSG00000124151 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y6Q9
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DHT

Query on DHT



Download:Ideal Coordinates CCD File
C [auth A]5-ALPHA-DIHYDROTESTOSTERONE
C19 H30 O2
NVKAWKQGWWIWPM-ABEVXSGRSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
DHT BindingDB:  3L3X Ki: min: 0.2, max: 10 (nM) from 12 assay(s)
Kd: 0.25 (nM) from 1 assay(s)
IC50: min: 0.05, max: 18.5 (nM) from 14 assay(s)
EC50: min: 0.05, max: 20 (nM) from 16 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free:  0.206 (Depositor), 0.211 (DCC) 
  • R-Value Work:  0.179 (Depositor), 0.191 (DCC) 
  • R-Value Observed: 0.181 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.314α = 90
b = 66.704β = 90
c = 73.137γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-01-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description
  • Version 1.3: 2024-10-16
    Changes: Data collection, Database references, Derived calculations, Structure summary