6DK0

Human sigma-1 receptor bound to NE-100


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.252 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Structural basis for sigma1receptor ligand recognition.

Schmidt, H.R.Betz, R.M.Dror, R.O.Kruse, A.C.

(2018) Nat Struct Mol Biol 25: 981-987

  • DOI: https://doi.org/10.1038/s41594-018-0137-2
  • Primary Citation of Related Structures:  
    6DJZ, 6DK0, 6DK1

  • PubMed Abstract: 

    The σ 1 receptor is a poorly understood membrane protein expressed throughout the human body. Ligands targeting the σ 1 receptor are in clinical trials for treatment of Alzheimer's disease, ischemic stroke, and neuropathic pain. However, relatively little is known regarding the σ 1 receptor's molecular function. Here, we present crystal structures of human σ 1 receptor bound to the antagonists haloperidol and NE-100, and the agonist (+)-pentazocine, at crystallographic resolutions of 3.1 Å, 2.9 Å, and 3.1 Å, respectively. These structures reveal a unique binding pose for the agonist. The structures and accompanying molecular dynamics (MD) simulations identify agonist-induced structural rearrangements in the receptor. Additionally, we show that ligand binding to σ 1 is a multistep process that is rate limited by receptor conformational change. We used MD simulations to reconstruct a ligand binding pathway involving two major conformational changes. These data provide a framework for understanding the molecular basis for σ 1 agonism.


  • Organizational Affiliation

    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sigma non-opioid intracellular receptor 1
A, B, C
227Homo sapiensMutation(s): 0 
Gene Names: SIGMAR1OPRS1SRBPAAG8
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q99720 (Homo sapiens)
Explore Q99720 
Go to UniProtKB:  Q99720
PHAROS:  Q99720
GTEx:  ENSG00000147955 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99720
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
OLC
Query on OLC

Download Ideal Coordinates CCD File 
AA [auth C]
BA [auth C]
CA [auth C]
DA [auth C]
EA [auth C]
AA [auth C],
BA [auth C],
CA [auth C],
DA [auth C],
EA [auth C],
L [auth A],
M [auth A],
N [auth A]
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
GKY
Query on GKY

Download Ideal Coordinates CCD File 
D [auth A],
O [auth B],
V [auth C]
N-{2-[4-methoxy-3-(2-phenylethoxy)phenyl]ethyl}-N-propylpropan-1-amine
C23 H33 N O2
YBLIQJGXRLZBCZ-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
P [auth B],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
W [auth C],
X [auth C],
Y [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
K [auth A],
U [auth B],
Z [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
GKY BindingDB:  6DK0 Ki: min: 1, max: 2.38 (nM) from 5 assay(s)
IC50: min: 1.3, max: 85 (nM) from 3 assay(s)
EC50: 1.07e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.252 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.556α = 90
b = 126.062β = 90
c = 109.702γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesDGE1745303
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM119185

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-17
    Type: Initial release
  • Version 1.1: 2019-11-27
    Changes: Author supporting evidence
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description