5OSB | pdb_00005osb

GLIC-GABAAR alpha1 chimera crystallized in complex with THDOC at pH4.5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 
    0.290 (Depositor), 0.298 (DCC) 
  • R-Value Work: 
    0.241 (Depositor), 0.249 (DCC) 
  • R-Value Observed: 
    0.244 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 5OSB

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Crystal structures of a GABAA-receptor chimera reveal new endogenous neurosteroid-binding sites.

Laverty, D.Thomas, P.Field, M.Andersen, O.J.Gold, M.G.Biggin, P.C.Gielen, M.Smart, T.G.

(2017) Nat Struct Mol Biol 24: 977-985

  • DOI: https://doi.org/10.1038/nsmb.3477
  • Primary Citation Related Structures: 
    5OSA, 5OSB, 5OSC

  • PubMed Abstract: 

    γ-Aminobutyric acid receptors (GABA A Rs) are vital for controlling excitability in the brain. This is emphasized by the numerous neuropsychiatric disorders that result from receptor dysfunction. A critical component of most native GABA A Rs is the α subunit. Its transmembrane domain is the target for many modulators, including endogenous brain neurosteroids that impact anxiety, stress and depression, and for therapeutic drugs, such as general anesthetics. Understanding the basis for the modulation of GABA A R function requires high-resolution structures. Here we present the first atomic structures of a GABA A R chimera at 2.8-Å resolution, including those bound with potentiating and inhibitory neurosteroids. These structures define new allosteric binding sites for these modulators that are associated with the α-subunit transmembrane domain. Our findings will enable the exploitation of neurosteroids for therapeutic drug design to regulate GABA A Rs in neurological disorders.


  • Organizational Affiliation
    • Department of Neuroscience, Physiology & Pharmacology, University College London, London, UK.

Macromolecule Content 

  • Total Structure Weight: 195.26 kDa 
  • Atom Count: 12,561 
  • Modeled Residue Count: 1,562 
  • Deposited Residue Count: 1,680 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Proton-gated ion channel,Gamma-aminobutyric acid receptor subunit alpha-1,Gamma-aminobutyric acid receptor subunit alpha-1
A, B, C, D, E
336Gloeobacter violaceus PCC 7421Mus musculusMutation(s): 0 
Gene Names: glvIglr4197Gabra1Gabra-1
Membrane Entity: Yes 
UniProt
Find proteins for P62812 (Mus musculus)
Explore P62812 
Go to UniProtKB:  P62812
Find proteins for Q7NDN8 (Gloeobacter violaceus (strain ATCC 29082 / PCC 7421))
Explore Q7NDN8 
Go to UniProtKB:  Q7NDN8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ7NDN8P62812
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A8Z

Query on A8Z



Download:Ideal Coordinates CCD File
F [auth A],
G [auth A],
J [auth B],
L [auth C],
P [auth E]
Tetrahydrodeoxycorticosterone
C21 H34 O3
CYKYBWRSLLXBOW-GDYGHMJCSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
H [auth A],
K [auth B],
M [auth C],
N [auth D],
Q [auth E]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL

Query on CL



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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free:  0.290 (Depositor), 0.298 (DCC) 
  • R-Value Work:  0.241 (Depositor), 0.249 (DCC) 
  • R-Value Observed: 0.244 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 185.218α = 90
b = 133.507β = 103.41
c = 162.263γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
PHASERphasing
Aimlessdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United KingdomMR/K005537/1
Royal SocietyUnited Kingdom104194/Z/14/Z
Engineering and Physical Sciences Research CouncilUnited KingdomEP/J003921/1
Engineering and Physical Sciences Research CouncilUnited KingdomEP/L000253/1

Revision History  (Full details and data files)

  • Version 1.0: 2017-10-11
    Type: Initial release
  • Version 1.1: 2017-11-15
    Changes: Database references
  • Version 1.2: 2018-01-31
    Changes: Author supporting evidence
  • Version 1.3: 2024-01-17
    Changes: Data collection, Database references, Refinement description