9FF2 | pdb_00009ff2

Cryo-EM structure of the beta3 homomeric GABA(A) receptor in complex with HSM in the long-lived symmetric desensitised state (C1)

PDB DOI: https://doi.org/10.2210/pdb9FF2/pdb
EM Map EMD-50349: EMDB EMDataResource

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

Deposited: 2024-05-21 Released: 2025-06-04
Deposition Author(s): Mihaylov, D.B., Malinauskas, T., Aricescu, A.R.
Funding Organization(s): Medical Research Council (MRC, United Kingdom), Cancer Research UK, National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.80 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Cryo-EM structure of the beta3 homomeric GABA(A) receptor in complex with HSM in the long-lived symmetric desensitised state (C1)

Mihaylov, D.B., Malinauskas, T., Aricescu, A.R.

To be published.

Macromolecule Content

Total Structure Weight: 238.87 kDa
Atom Count: 14,680
Modeled Residue Count: 1,685
Deposited Residue Count: 1,975
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gamma-aminobutyric acid receptor subunit beta-3	A, B, C, D, E	395	Homo sapiens	Mutation(s): 0 Gene Names: GABRB3 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P28472 (Homo sapiens) Explore P28472 Go to UniProtKB: P28472
PHAROS: P28472 GTEx: ENSG00000166206
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P28472
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain D Focus chain E	Go to GlyGen: P28472-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F [auth a], H [auth b], J [auth c], L [auth d], N [auth e]	5		N-Glycosylation	Interactions Focus chain F [auth a] Focus chain H [auth b] Focus chain J [auth c] Focus chain L [auth d] Focus chain N [auth e] Interactions & Density Focus chain F [auth a] Focus chain H [auth b] Focus chain J [auth c] Focus chain L [auth d] Focus chain N [auth e]
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G [auth F], I [auth G], K [auth H], M [auth I], O [auth J]	2		N-Glycosylation	Interactions Focus chain G [auth F] Focus chain I [auth G] Focus chain K [auth H] Focus chain M [auth I] Focus chain O [auth J] Interactions & Density Focus chain G [auth F] Focus chain I [auth G] Focus chain K [auth H] Focus chain M [auth I] Focus chain O [auth J]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain HA [auth C] SDF format, chain P [auth A] SDF format, chain SA [auth E] SDF format, chain MA [auth D] MOL2 format, chain AA [auth B] MOL2 format, chain HA [auth C] MOL2 format, chain P [auth A] MOL2 format, chain SA [auth E] MOL2 format, chain MA [auth D] mmCIF format, chain AA [auth B] mmCIF format, chain HA [auth C] mmCIF format, chain P [auth A] mmCIF format, chain SA [auth E] mmCIF format, chain MA [auth D]	AA [auth B], HA [auth C], MA [auth D], P [auth A], SA [auth E]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth B] Focus chain HA [auth C] Focus chain MA [auth D] Focus chain P [auth A] Focus chain SA [auth E] Interactions & Density Focus chain AA [auth B] Focus chain HA [auth C] Focus chain MA [auth D] Focus chain P [auth A] Focus chain SA [auth E]
D10 Query on D10 Download Ideal Coordinates CCD File SDF format, chain DA [auth C] SDF format, chain JA [auth D] SDF format, chain OA [auth E] SDF format, chain QA [auth E] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] SDF format, chain T [auth A] SDF format, chain PA [auth E] SDF format, chain KA [auth D] SDF format, chain FA [auth C] SDF format, chain EA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain JA [auth D] MOL2 format, chain OA [auth E] MOL2 format, chain QA [auth E] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain T [auth A] MOL2 format, chain PA [auth E] MOL2 format, chain KA [auth D] MOL2 format, chain FA [auth C] MOL2 format, chain EA [auth C] mmCIF format, chain DA [auth C] mmCIF format, chain JA [auth D] mmCIF format, chain OA [auth E] mmCIF format, chain QA [auth E] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain T [auth A] mmCIF format, chain PA [auth E] mmCIF format, chain KA [auth D] mmCIF format, chain FA [auth C] mmCIF format, chain EA [auth C]	DA [auth C] EA [auth C] FA [auth C] JA [auth D] KA [auth D] DA [auth C], EA [auth C], FA [auth C], JA [auth D], KA [auth D], OA [auth E], PA [auth E], QA [auth E], R [auth A], S [auth A], T [auth A], W [auth B], X [auth B], Y [auth B], Z [auth B]	DECANE C₁₀ H₂₂ DIOQZVSQGTUSAI-UHFFFAOYSA-N		Interactions Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain OA [auth E] Focus chain PA [auth E] Focus chain QA [auth E] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain OA [auth E] Focus chain PA [auth E] Focus chain QA [auth E] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
HSM (Subject of Investigation/LOI) Query on HSM Download Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain IA [auth D] SDF format, chain NA [auth E] SDF format, chain Q [auth A] SDF format, chain V [auth B] MOL2 format, chain CA [auth C] MOL2 format, chain IA [auth D] MOL2 format, chain NA [auth E] MOL2 format, chain Q [auth A] MOL2 format, chain V [auth B] mmCIF format, chain CA [auth C] mmCIF format, chain IA [auth D] mmCIF format, chain NA [auth E] mmCIF format, chain Q [auth A] mmCIF format, chain V [auth B]	CA [auth C], IA [auth D], NA [auth E], Q [auth A], V [auth B]	HISTAMINE C₅ H₉ N₃ NTYJJOPFIAHURM-UHFFFAOYSA-N		Interactions Focus chain CA [auth C] Focus chain IA [auth D] Focus chain NA [auth E] Focus chain Q [auth A] Focus chain V [auth B] Interactions & Density Focus chain CA [auth C] Focus chain IA [auth D] Focus chain NA [auth E] Focus chain Q [auth A] Focus chain V [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain BA [auth B] SDF format, chain GA [auth C] SDF format, chain RA [auth E] SDF format, chain U [auth A] SDF format, chain LA [auth D] MOL2 format, chain BA [auth B] MOL2 format, chain GA [auth C] MOL2 format, chain RA [auth E] MOL2 format, chain U [auth A] MOL2 format, chain LA [auth D] mmCIF format, chain BA [auth B] mmCIF format, chain GA [auth C] mmCIF format, chain RA [auth E] mmCIF format, chain U [auth A] mmCIF format, chain LA [auth D]	BA [auth B], GA [auth C], LA [auth D], RA [auth E], U [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain BA [auth B] Focus chain GA [auth C] Focus chain LA [auth D] Focus chain RA [auth E] Focus chain U [auth A] Interactions & Density Focus chain BA [auth B] Focus chain GA [auth C] Focus chain LA [auth D] Focus chain RA [auth E] Focus chain U [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.80 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21_5207
RECONSTRUCTION	cryoSPARC

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-06-04

Deposition Author(s):

Mihaylov, D.B.

Malinauskas, T.

Aricescu, A.R.

Funding Organization	Location	Grant Number
Medical Research Council (MRC, United Kingdom)	United Kingdom	MC_UP_1201/15
Cancer Research UK	United Kingdom	DRCRPG-May23/100002
Medical Research Council (MRC, United Kingdom)	United Kingdom	MR/L009609/1
Medical Research Council (MRC, United Kingdom)	United Kingdom	MC_EX_MR/T046279/1
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	1R01-GM135550
National Science Foundation (NSF, United States)	United States	NeuroNex 2014862