5O8F

Structure of a chimaeric beta3-alpha5 GABAA receptor in complex with nanobody Nb25 and pregnanolone


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.232 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis for GABAA receptor potentiation by neurosteroids.

Miller, P.S.Scott, S.Masiulis, S.De Colibus, L.Pardon, E.Steyaert, J.Aricescu, A.R.

(2017) Nat. Struct. Mol. Biol. 24: 986-992

  • DOI: 10.1038/nsmb.3484
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Type A γ-aminobutyric acid receptors (GABA <sub>A </sub>Rs) are the principal mediators of inhibitory neurotransmission in the human brain. Endogenous neurosteroids interact with GABA <sub>A </sub>Rs to regulate acute and chronic anxiety and are pote ...

    Type A γ-aminobutyric acid receptors (GABA A Rs) are the principal mediators of inhibitory neurotransmission in the human brain. Endogenous neurosteroids interact with GABA A Rs to regulate acute and chronic anxiety and are potent sedative, analgesic, anticonvulsant and anesthetic agents. Their mode of binding and mechanism of receptor potentiation, however, remain unknown. Here we report crystal structures of a chimeric GABA A R construct in apo and pregnanolone-bound states. The neurosteroid-binding site is mechanically coupled to the helices lining the ion channel pore and modulates the desensitization-gate conformation. We demonstrate that the equivalent site is responsible for physiological, heteromeric GABA A R potentiation and explain the contrasting modulatory properties of 3a versus 3b neurosteroid epimers. These results illustrate how peripheral lipid ligands can regulate the desensitization gate of GABA A Rs, a process of broad relevance to pentameric ligand-gated ion channels.


    Organizational Affiliation

    Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge, UK.,VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium.,Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels, Belgium.,Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Gamma-aminobutyric acid receptor subunit beta-3,Gamma-aminobutyric acid receptor subunit alpha-5,Gamma-aminobutyric acid receptor subunit alpha-5
A, B, C, D, E
367Homo sapiensMutation(s): 0 
Gene Names: GABRB3, GABRA5
Find proteins for P28472 (Homo sapiens)
Go to Gene View: GABRB3
Go to UniProtKB:  P28472
Find proteins for P31644 (Homo sapiens)
Go to Gene View: GABRA5
Go to UniProtKB:  P31644
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Nanobody Nb25
K, O
125N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Nanobody Nb25
L, M, N
124N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN

Download SDF File 
Download CCD File 
A, B, C, D, E
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BMA
Query on BMA

Download SDF File 
Download CCD File 
A, B, C, D, E
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B, C, D, E
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
P9N
Query on P9N

Download SDF File 
Download CCD File 
B, C, D, E
Pregnanolone
(3alpha,5beta)-3-Hydroxypregnan-20-one
C21 H34 O2
AURFZBICLPNKBZ-YZRLXODZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.232 
  • Space Group: I 2 3
Unit Cell:
Length (Å)Angle (°)
a = 290.102α = 90.00
b = 290.102β = 90.00
c = 290.102γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
PHASERphasing
Aimlessdata scaling
Cootmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/M024709/1
Medical Research Council (United Kingdom)United KingdomMR/L009609/1
Medical Research Council (United Kingdom)United KingdomMC_UP_1201/15
Wellcome TrustUnited Kingdom105247/Z/14/Z
Human Frontier Science ProgramFranceRGP0065/2014
Wellcome TrustUnited Kingdom090532/Z/09/Z

Revision History 

  • Version 1.0: 2017-11-01
    Type: Initial release
  • Version 1.1: 2017-11-15
    Type: Database references