8OQ7

CryoEM structure of human rho1 GABAA receptor in complex with inhibitor TPMPA


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structure and dynamics of differential ligand binding in the human rho-type GABA A receptor.

Cowgill, J.Fan, C.Haloi, N.Tobiasson, V.Zhuang, Y.Howard, R.J.Lindahl, E.

(2023) Neuron 111: 3450

  • DOI: https://doi.org/10.1016/j.neuron.2023.08.006
  • Primary Citation of Related Structures:  
    8OP9, 8OQ6, 8OQ7, 8OQ8, 8OQA

  • PubMed Abstract: 

    The neurotransmitter γ-aminobutyric acid (GABA) drives critical inhibitory processes in and beyond the nervous system, partly via ionotropic type-A receptors (GABA A Rs). Pharmacological properties of ρ-type GABA A Rs are particularly distinctive, yet the structural basis for their specialization remains unclear. Here, we present cryo-EM structures of a lipid-embedded human ρ1 GABA A R, including a partial intracellular domain, under apo, inhibited, and desensitized conditions. An apparent resting state, determined first in the absence of modulators, was recapitulated with the specific inhibitor (1,2,5,6-tetrahydropyridin-4-yl)methylphosphinic acid and blocker picrotoxin and provided a rationale for bicuculline insensitivity. Comparative structures, mutant recordings, and molecular simulations with and without GABA further explained the sensitized but slower activation of ρ1 relative to canonical subtypes. Combining GABA with picrotoxin also captured an apparent uncoupled intermediate state. This work reveals structural mechanisms of gating and modulation with applications to ρ-specific pharmaceutical design and to our biophysical understanding of ligand-gated ion channels.


  • Organizational Affiliation

    Department of Biochemistry and Biophysics, SciLifeLab, Stockholm University, 17121 Solna, Sweden.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Gamma-aminobutyric acid receptor subunit rho-1
A, B, C, D, E
479Homo sapiensMutation(s): 0 
Gene Names: GABRR1
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P24046 (Homo sapiens)
Explore P24046 
Go to UniProtKB:  P24046
PHAROS:  P24046
GTEx:  ENSG00000146276 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP24046
Glycosylation
Glycosylation Sites: 2Go to GlyGen: P24046-1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
BB [auth E]
CB [auth E]
FA [auth C]
G [auth A]
GA [auth C]
BB [auth E],
CB [auth E],
FA [auth C],
G [auth A],
GA [auth C],
H [auth A],
QA [auth D],
RA [auth D],
T [auth B],
U [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
D12
Query on D12

Download Ideal Coordinates CCD File 
BA [auth B]
HB [auth E]
JB [auth E]
LA [auth C]
M [auth A]
BA [auth B],
HB [auth E],
JB [auth E],
LA [auth C],
M [auth A],
NA [auth C],
O [auth A],
WA [auth D],
YA [auth D],
Z [auth B]
DODECANE
C12 H26
SNRUBQQJIBEYMU-UHFFFAOYSA-N
VZA (Subject of Investigation/LOI)
Query on VZA

Download Ideal Coordinates CCD File 
AB [auth E],
EA [auth C],
F [auth A],
PA [auth D],
S [auth B]
methyl(1,2,3,6-tetrahydropyridin-4-yl)phosphinic acid
C6 H12 N O2 P
MFUKVPOVVKKLRQ-UHFFFAOYSA-N
D10
Query on D10

Download Ideal Coordinates CCD File 
AA [auth B]
DA [auth C]
IB [auth E]
MA [auth C]
N [auth A]
AA [auth B],
DA [auth C],
IB [auth E],
MA [auth C],
N [auth A],
OA [auth D],
P [auth A],
R [auth B],
XA [auth D],
ZA [auth E]
DECANE
C10 H22
DIOQZVSQGTUSAI-UHFFFAOYSA-N
OCT
Query on OCT

Download Ideal Coordinates CCD File 
GB [auth E],
KA [auth C],
L [auth A],
VA [auth D],
Y [auth B]
N-OCTANE
C8 H18
TVMXDCGIABBOFY-UHFFFAOYSA-N
HEX
Query on HEX

Download Ideal Coordinates CCD File 
DB [auth E]
EB [auth E]
FB [auth E]
HA [auth C]
I [auth A]
DB [auth E],
EB [auth E],
FB [auth E],
HA [auth C],
I [auth A],
IA [auth C],
J [auth A],
JA [auth C],
K [auth A],
SA [auth D],
TA [auth D],
UA [auth D],
V [auth B],
W [auth B],
X [auth B]
HEXANE
C6 H14
VLKZOEOYAKHREP-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
CA [auth B],
Q [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Binding Affinity Annotations 
IDSourceBinding Affinity
VZA BindingDB:  8OQ7 IC50: 2220 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Research CouncilSweden2019-02433

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-30
    Type: Initial release
  • Version 1.1: 2023-09-13
    Changes: Database references
  • Version 1.2: 2023-11-15
    Changes: Database references
  • Version 1.3: 2024-02-07
    Changes: Structure summary
  • Version 1.4: 2024-10-16
    Changes: Data collection, Structure summary