9FRB | pdb_00009frb

CryoEM structure of human rho1 GABAA receptor in complex with CGP36742


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.05 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Cryo-EM structures of rho 1 GABA A receptors with antagonist and agonist drugs.

Fan, C.Cowgill, J.Howard, R.J.Lindahl, E.

(2025) Nat Commun 16: 7077-7077

  • DOI: https://doi.org/10.1038/s41467-025-61932-6
  • Primary Citation of Related Structures:  
    9FRB, 9FRE, 9FRF, 9FRG, 9FRH, 9FRI

  • PubMed Abstract: 

    The family of ρ-type GABA A receptors includes potential therapeutic targets in several neurological conditions, and features distinctive pharmacology compared to other subtypes. Here we report four cryo-EM structures with previously unresolved ligands, electrophysiology recordings, and molecular dynamics simulations to characterize binding and conformational impact of the drugs THIP (a non-opioid analgesic), CGP36742 (a phosphinic acid) and GABOB (an anticonvulsant) on a human ρ1 GABA A receptor. A distinctive binding pose of THIP in ρ1 versus α4β3δ GABA A receptors offers a rationale for its inverse effects on these subtypes. CGP36742 binding is similar to the canonical ρ-type inhibitor TPMPA, supporting a shared mechanism of action among phosphinic acids. Binding of GABOB is similar to GABA, but produces a mixture of partially-locked and desensitized states, likely underlying weaker agonist activity. Together, these results elucidate interactions of a ρ-type GABA A receptor with therapeutic drugs, offering mechanistic insights and a basis for further pharmaceutical development.


  • Organizational Affiliation

    Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Solna, Sweden. chf4001@kth.se.


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
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: 1Go 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]
EA [auth C]
FA [auth C]
G [auth A]
BB [auth E],
CB [auth E],
EA [auth C],
FA [auth C],
G [auth A],
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
A1IFA (Subject of Investigation/LOI)
Query on A1IFA

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AB [auth E],
DA [auth C],
F [auth A],
PA [auth D],
S [auth B]
3-azanylpropyl(butyl)phosphinic acid
C7 H18 N O2 P
ONNMDRQRSGKZCN-UHFFFAOYSA-N
D12
Query on D12

Download Ideal Coordinates CCD File 
BA [auth B]
HB [auth E]
JB [auth E]
KA [auth C]
M [auth A]
BA [auth B],
HB [auth E],
JB [auth E],
KA [auth C],
M [auth A],
MA [auth C],
O [auth A],
WA [auth D],
YA [auth D],
Z [auth B]
DODECANE
C12 H26
SNRUBQQJIBEYMU-UHFFFAOYSA-N
D10
Query on D10

Download Ideal Coordinates CCD File 
AA [auth B]
CA [auth C]
IB [auth E]
LA [auth C]
N [auth A]
AA [auth B],
CA [auth C],
IB [auth E],
LA [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

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GB [auth E],
JA [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]
GA [auth C]
HA [auth C]
DB [auth E],
EB [auth E],
FB [auth E],
GA [auth C],
HA [auth C],
I [auth A],
IA [auth C],
J [auth A],
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 
NA [auth C],
Q [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.05 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

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: 2025-07-02
    Type: Initial release
  • Version 1.1: 2025-08-13
    Changes: Data collection, Database references