8RHG | pdb_00008rhg

CryoEM structure of human rho1 GABAA receptor in complex with GABA and pregnenolone sulfate

PDB DOI: https://doi.org/10.2210/pdb8RHG/pdb
EM Map EMD-19175: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No
Membrane Protein: Yes PDBTM MemProtMD

Deposited: 2023-12-15 Released: 2024-08-28
Deposition Author(s): Chen, F., John, C., Rebecca, J.H., Erik, L.
Funding Organization(s): Swedish Research Council

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.01 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 8RHG

This is version 1.2 of the entry. See complete history.

Literature

Divergent mechanisms of steroid inhibition in the human rho1 GABAA receptor

Chen, F., John, C., Rebecca, J.H., Erik, L.

(2024) Nat Commun

Macromolecule Content

Total Structure Weight: 283.83 kDa
Atom Count: 13,897
Modeled Residue Count: 1,650
Deposited Residue Count: 2,395
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gamma-aminobutyric acid receptor subunit rho-1	A, B, C, D, E	479	Homo sapiens	Mutation(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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P24046
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain B Focus chain D Focus chain E	Go to GlyGen: P24046-1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A8W Query on A8W Download:Ideal Coordinates CCD File SDF format, chain K [auth A] MOL2 format, chain K [auth A] mmCIF format, chain K [auth A]	K [auth A]	Pregnenolone sulfate C₂₁ H₃₂ O₅ S DIJBBUIOWGGQOP-QGVNFLHTSA-N		Interactions Focus chain K [auth A] Interactions & Density Focus chain K [auth A]
NAG (Subject of Investigation/LOI) Query on NAG Download:Ideal Coordinates CCD File SDF format, chain X [auth D] SDF format, chain W [auth D] SDF format, chain S [auth C] SDF format, chain R [auth C] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain BA [auth E] SDF format, chain AA [auth E] MOL2 format, chain X [auth D] MOL2 format, chain W [auth D] MOL2 format, chain S [auth C] MOL2 format, chain R [auth C] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain BA [auth E] MOL2 format, chain AA [auth E] mmCIF format, chain X [auth D] mmCIF format, chain W [auth D] mmCIF format, chain S [auth C] mmCIF format, chain R [auth C] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain BA [auth E] mmCIF format, chain AA [auth E]	AA [auth E] BA [auth E] G [auth A] H [auth A] M [auth B] AA [auth E], BA [auth E], G [auth A], H [auth A], M [auth B], N [auth B], R [auth C], S [auth C], W [auth D], X [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth E] Focus chain BA [auth E] Focus chain G [auth A] Focus chain H [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain W [auth D] Focus chain X [auth D] Interactions & Density Focus chain AA [auth E] Focus chain BA [auth E] Focus chain G [auth A] Focus chain H [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain W [auth D] Focus chain X [auth D]
OCT Query on OCT Download:Ideal Coordinates CCD File SDF format, chain Y [auth D] SDF format, chain T [auth C] SDF format, chain O [auth B] SDF format, chain I [auth A] SDF format, chain CA [auth E] MOL2 format, chain Y [auth D] MOL2 format, chain T [auth C] MOL2 format, chain O [auth B] MOL2 format, chain I [auth A] MOL2 format, chain CA [auth E] mmCIF format, chain Y [auth D] mmCIF format, chain T [auth C] mmCIF format, chain O [auth B] mmCIF format, chain I [auth A] mmCIF format, chain CA [auth E]	CA [auth E], I [auth A], O [auth B], T [auth C], Y [auth D]	N-OCTANE C₈ H₁₈ TVMXDCGIABBOFY-UHFFFAOYSA-N		Interactions Focus chain CA [auth E] Focus chain I [auth A] Focus chain O [auth B] Focus chain T [auth C] Focus chain Y [auth D] Interactions & Density Focus chain CA [auth E] Focus chain I [auth A] Focus chain O [auth B] Focus chain T [auth C] Focus chain Y [auth D]
ABU Query on ABU Download:Ideal Coordinates CCD File SDF format, chain V [auth D] SDF format, chain Q [auth C] SDF format, chain L [auth B] SDF format, chain J [auth A] SDF format, chain F [auth A] MOL2 format, chain V [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain L [auth B] MOL2 format, chain J [auth A] MOL2 format, chain F [auth A] mmCIF format, chain V [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain L [auth B] mmCIF format, chain J [auth A] mmCIF format, chain F [auth A]	F [auth A], J [auth A], L [auth B], Q [auth C], V [auth D]	GAMMA-AMINO-BUTANOIC ACID C₄ H₉ N O₂ BTCSSZJGUNDROE-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain J [auth A] Focus chain L [auth B] Focus chain Q [auth C] Focus chain V [auth D] Interactions & Density Focus chain F [auth A] Focus chain J [auth A] Focus chain L [auth B] Focus chain Q [auth C] Focus chain V [auth D]
HEX Query on HEX Download:Ideal Coordinates CCD File SDF format, chain Z [auth D] SDF format, chain U [auth C] SDF format, chain P [auth B] SDF format, chain DA [auth E] MOL2 format, chain Z [auth D] MOL2 format, chain U [auth C] MOL2 format, chain P [auth B] MOL2 format, chain DA [auth E] mmCIF format, chain Z [auth D] mmCIF format, chain U [auth C] mmCIF format, chain P [auth B] mmCIF format, chain DA [auth E]	DA [auth E], P [auth B], U [auth C], Z [auth D]	HEXANE C₆ H₁₄ VLKZOEOYAKHREP-UHFFFAOYSA-N		Interactions Focus chain DA [auth E] Focus chain P [auth B] Focus chain U [auth C] Focus chain Z [auth D] Interactions & Density Focus chain DA [auth E] Focus chain P [auth B] Focus chain U [auth C] Focus chain Z [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain EA [auth E] MOL2 format, chain EA [auth E] mmCIF format, chain EA [auth E]	EA [auth E]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain EA [auth E] Interactions & Density Focus chain EA [auth E]

Binding Affinity Annotations
ID	Source	Binding Affinity
ABU	BindingDB: 8RHG	EC50: min: 269, max: 1190 (nM) from 7 assay(s)

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.01 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2024-08-28

Deposition Author(s):

Funding Organization	Location	Grant Number
Swedish Research Council	Sweden	--

Revision History (Full details and data files)

Version 1.0: 2024-08-28
Type: Initial release
Version 1.1: 2024-11-20
Changes: Data collection, Structure summary
Version 1.2: 2025-07-09
Changes: Data collection

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.