7NDO | pdb_00007ndo

ER-PRS*(-) (L536S, L372R) in complex with raloxifene


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 
    0.195 (Depositor), 0.196 (DCC) 
  • R-Value Work: 
    0.185 (Depositor), 0.187 (DCC) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 7NDO

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

A PROSS-designed extensively mutated estrogen receptor alpha variant displays enhanced thermal stability while retaining native allosteric regulation and structure.

Kriegel, M.Wiederanders, H.J.Alkhashrom, S.Eichler, J.Muller, Y.A.

(2021) Sci Rep 11: 10509-10509

  • DOI: https://doi.org/10.1038/s41598-021-89785-1
  • Primary Citation Related Structures: 
    7NDO, 7NEL, 7NFB

  • PubMed Abstract: 

    Protein stability limitations often hamper the exploration of proteins as drug targets. Here, we show that the application of PROSS server algorithms to the ligand-binding domain of human estrogen receptor alpha (hERα) enabled the development of variant ER PRS* that comprises 24 amino acid substitutions and exhibits multiple improved characteristics. The protein displays enhanced production rates in E. coli, crystallizes readily and its thermal stability is increased significantly by 23 °C. hERα is a nuclear receptor (NR) family member. In NRs, protein function is allosterically regulated by its interplay with small molecule effectors and the interaction with coregulatory proteins. The in-depth characterization of ER PRS* shows that these cooperative effects are fully preserved despite that 10% of all residues were substituted . Crystal structures reveal several salient features, i.e. the introduction of a tyrosine corner in a helix-loop-helix segment and the formation of a novel surface salt bridge network possibly explaining the enhanced thermal stability. ER PRS* shows that prior successes in computational approaches for stabilizing proteins can be extended to proteins with complex allosteric regulatory behaviors as present in NRs. Since NRs including hERα are implicated in multiple diseases, our ER PRS* variant shows significant promise for facilitating the development of novel hERα modulators.


  • Organizational Affiliation
    • Division of Biotechnology, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany.

Macromolecule Content 

  • Total Structure Weight: 58.5 kDa 
  • Atom Count: 4,255 
  • Modeled Residue Count: 469 
  • Deposited Residue Count: 494 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Estrogen receptor
A, B
247Homo sapiensMutation(s): 29 
Gene Names: ESR1ESRNR3A1
UniProt & NIH Common Fund Data Resources
Find proteins for P03372 (Homo sapiens)
Explore P03372 
Go to UniProtKB:  P03372
PHAROS:  P03372
GTEx:  ENSG00000091831 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03372
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
RAL
(Subject of Investigation/LOI)

Query on RAL



Download:Ideal Coordinates CCD File
C [auth A],
J [auth B]
RALOXIFENE
C28 H27 N O4 S
GZUITABIAKMVPG-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
D [auth A]
E [auth A]
F [auth A]
K [auth B]
L [auth B]
D [auth A],
E [auth A],
F [auth A],
K [auth B],
L [auth B],
M [auth B],
N [auth B],
O [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
G [auth A],
H [auth A],
I [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free:  0.195 (Depositor), 0.196 (DCC) 
  • R-Value Work:  0.185 (Depositor), 0.187 (DCC) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.581α = 97.839
b = 51.787β = 113.516
c = 57.513γ = 110.417
Software Package:
Software NamePurpose
PHENIXrefinement
MxCuBEdata collection
XDSdata processing
PHENIXphasing
XDSdata reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-08-25
    Type: Initial release
  • Version 1.1: 2022-10-26
    Changes: Derived calculations
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description