7W2C

The closed conformation of the sigma-1 receptor from Xenopus laevis complexed with PRE084


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.33 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.231 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

An open-like conformation of the sigma-1 receptor reveals its ligand entry pathway.

Meng, F.Xiao, Y.Ji, Y.Sun, Z.Zhou, X.

(2022) Nat Commun 13: 1267-1267

  • DOI: https://doi.org/10.1038/s41467-022-28946-w
  • Primary Citation of Related Structures:  
    7W2B, 7W2C, 7W2D, 7W2E, 7W2F, 7W2G, 7W2H

  • PubMed Abstract: 

    The sigma-1 receptor (σ 1 R) is a non-opioid transmembrane receptor which has been implicated in many diseases, including neurodegenerative disorders and cancer. After more than forty years of research, substantial progress has been made in understanding this unique receptor, yet the molecular mechanism of its ligand entry pathway remains uncertain. Published structures of human σ 1 R reveal its homotrimeric organization of a cupin-fold β-barrel body that contains the ligand binding site, a carboxy-terminal V-shaped two-helix bundle, and a single amino-terminal transmembrane helix, while simulation studies have suggested a ligand entry pathway that is generated by conformational rearrangements of the cupin-fold domain. Here, we present multiple crystal structures, including an open-like conformation, of σ 1 R from Xenopus laevis. Together with functional binding analysis our data suggest that access to the σ 1 R ligand binding site is likely achieved by protein conformational changes that involve the carboxy-terminal two-helix bundle, rather than structural changes in the cupin-fold domain.


  • Organizational Affiliation

    Department of Integrated Traditional Chinese and Western Medicine, Rare Diseases Center, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sigma non-opioid intracellular receptor 1225Xenopus laevisMutation(s): 0 
Gene Names: sigmar1oprs1
Membrane Entity: Yes 
UniProt
Find proteins for Q6DCU6 (Xenopus laevis)
Explore Q6DCU6 
Go to UniProtKB:  Q6DCU6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6DCU6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
E84 (Subject of Investigation/LOI)
Query on E84

Download Ideal Coordinates CCD File 
BA [auth D]
FA [auth F]
IA [auth G]
LA [auth H]
O [auth A]
BA [auth D],
FA [auth F],
IA [auth G],
LA [auth H],
O [auth A],
OA [auth I],
RA [auth J],
S [auth C],
V [auth E],
VA [auth K],
Y [auth B],
YA [auth L]
2-morpholin-4-ylethyl 1-phenylcyclohexane-1-carboxylate
C19 H27 N O3
RQHKZUBCUZVZEF-UHFFFAOYSA-N
BOG
Query on BOG

Download Ideal Coordinates CCD File 
CA [auth D],
P [auth A],
SA [auth J]
octyl beta-D-glucopyranoside
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
AU
Query on AU

Download Ideal Coordinates CCD File 
AA [auth D]
DA [auth F]
EA [auth F]
GA [auth G]
HA [auth G]
AA [auth D],
DA [auth F],
EA [auth F],
GA [auth G],
HA [auth G],
JA [auth H],
KA [auth H],
M [auth A],
MA [auth I],
N [auth A],
NA [auth I],
PA [auth J],
Q [auth C],
QA [auth J],
R [auth C],
T [auth E],
TA [auth K],
U [auth E],
UA [auth K],
W [auth B],
WA [auth L],
X [auth B],
XA [auth L],
Z [auth D]
GOLD ION
Au
ZBKIUFWVEIBQRT-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.33 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.231 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.155α = 90
b = 148.78β = 92.76
c = 172.756γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31770783

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-16
    Type: Initial release
  • Version 1.1: 2022-03-23
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description