9FAM | pdb_00009fam

CryoEM structure of human full-length alpha1beta3gamma2 GABA(A)R in complex with GARLH4, the TMD of Neuroligin2, GABA and Megabody38 in a desensitised state (StateD3)

PDB DOI: https://doi.org/10.2210/pdb9FAM/pdb
EM Map EMD-50275: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens, Lama glama
Expression System: Homo sapiens, Escherichia coli
Mutation(s): No

Deposited: 2024-05-10 Released: 2025-07-02
Deposition Author(s): Kasaragod, V.B., Aricescu, A.R.
Funding Organization(s): Medical Research Council (MRC, United Kingdom), European Molecular Biology Organization (EMBO), H2020 Marie Curie Actions of the European Commission, 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: 3.50 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

CryoEM structure of human full-length alpha1beta3gamma2 GABA(A)R in complex with GARLH4, the TMD of Neuroligin2, GABA and Megabody in a desensitised state (StateD3)

Kasaragod, V.B., Aricescu, A.R.

To be published.

Macromolecule Content

Total Structure Weight: 337.78 kDa
Atom Count: 17,822
Modeled Residue Count: 2,101
Deposited Residue Count: 2,878
Unique protein chains: 6

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gamma-aminobutyric acid receptor subunit alpha-1	A, C [auth D]	413	Homo sapiens	Mutation(s): 0 Gene Names: GABRA1
UniProt & NIH Common Fund Data Resources
Find proteins for P14867 (Homo sapiens) Explore P14867 Go to UniProtKB: P14867
PHAROS: P14867 GTEx: ENSG00000022355
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P14867
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Gamma-aminobutyric acid receptor subunit beta-3	B, D [auth E]	441	Homo sapiens	Mutation(s): 0 Gene Names: GABRB3
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: 2	Glycosylation Focus chain B Focus chain D [auth E]	Go to GlyGen: P28472-1
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform 2 of Gamma-aminobutyric acid receptor subunit gamma-2	E [auth C]	405	Homo sapiens	Mutation(s): 0 Gene Names: GABRG2
UniProt & NIH Common Fund Data Resources
Find proteins for P18507 (Homo sapiens) Explore P18507 Go to UniProtKB: P18507
PHAROS: P18507 GTEx: ENSG00000113327
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P18507
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain E [auth C]	Go to GlyGen: P18507-1
Sequence Annotations Expand
Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Neuroligin-2	F [auth H]	33	Homo sapiens	Mutation(s): 0 Gene Names: NLGN2, KIAA1366
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NFZ4 (Homo sapiens) Explore Q8NFZ4 Go to UniProtKB: Q8NFZ4
PHAROS: Q8NFZ4 GTEx: ENSG00000169992
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8NFZ4
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
LHFPL tetraspan subfamily member 4 protein	G [auth L]	193	Homo sapiens	Mutation(s): 0 Gene Names: LHFPL4, GARLH4
UniProt & NIH Common Fund Data Resources
Find proteins for Q7Z7J7 (Homo sapiens) Explore Q7Z7J7 Go to UniProtKB: Q7Z7J7
PHAROS: Q7Z7J7 GTEx: ENSG00000156959
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7Z7J7
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Megabody38	H [auth G]	539	Lama glama	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[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	I [auth F]	10		N/A	Interactions Focus chain I [auth F] Interactions & Density Focus chain I [auth F]
Glycosylation Resources
GlyTouCan: G40702WU GlyCosmos: G40702WU GlyGen: G40702WU

Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	J [auth I], N	3		N-Glycosylation	Interactions Focus chain J [auth I] Focus chain N Interactions & Density Focus chain J [auth I] Focus chain N
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 9
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	K [auth J], M	6		N-Glycosylation	Interactions Focus chain K [auth J] Focus chain M Interactions & Density Focus chain K [auth J] Focus chain M
Glycosylation Resources
GlyTouCan: G09724ZC GlyCosmos: G09724ZC GlyGen: G09724ZC

Entity ID: 10
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-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	L [auth K]	6		N/A	Interactions Focus chain L [auth K] Interactions & Density Focus chain L [auth K]
Glycosylation Resources
GlyTouCan: G56014GC GlyCosmos: G56014GC GlyGen: G56014GC

Entity ID: 11
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	O	2		N-Glycosylation	Interactions Focus chain O Interactions & Density Focus chain O
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGW Query on PGW Download Ideal Coordinates CCD File SDF format, chain GA [auth L] SDF format, chain FA [auth L] MOL2 format, chain GA [auth L] MOL2 format, chain FA [auth L] mmCIF format, chain GA [auth L] mmCIF format, chain FA [auth L]	FA [auth L], GA [auth L]	(1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate C₄₀ H₇₇ O₁₀ P PAZGBAOHGQRCBP-HGWHEPCSSA-N		Interactions Focus chain FA [auth L] Focus chain GA [auth L] Interactions & Density Focus chain FA [auth L] Focus chain GA [auth L]
PIO Query on PIO Download Ideal Coordinates CCD File SDF format, chain V [auth D] SDF format, chain P [auth A] MOL2 format, chain V [auth D] MOL2 format, chain P [auth A] mmCIF format, chain V [auth D] mmCIF format, chain P [auth A]	P [auth A], V [auth D]	[(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate C₂₅ H₄₉ O₁₉ P₃ XLNCEHRXXWQMPK-MJUMVPIBSA-N		Interactions Focus chain P [auth A] Focus chain V [auth D] Interactions & Density Focus chain P [auth A] Focus chain V [auth D]
CLR (Subject of Investigation/LOI) Query on CLR Download Ideal Coordinates CCD File SDF format, chain EA [auth C] MOL2 format, chain EA [auth C] mmCIF format, chain EA [auth C]	EA [auth C]	CHOLESTEROL C₂₇ H₄₆ O HVYWMOMLDIMFJA-DPAQBDIFSA-N		Interactions Focus chain EA [auth C] Interactions & Density Focus chain EA [auth C]
PLM Query on PLM Download Ideal Coordinates CCD File SDF format, chain DA [auth C] MOL2 format, chain DA [auth C] mmCIF format, chain DA [auth C]	DA [auth C]	PALMITIC ACID C₁₆ H₃₂ O₂ IPCSVZSSVZVIGE-UHFFFAOYSA-N		Interactions Focus chain DA [auth C] Interactions & Density Focus chain DA [auth C]
D10 Query on D10 Download Ideal Coordinates CCD File SDF format, chain Z [auth E] MOL2 format, chain Z [auth E] mmCIF format, chain Z [auth E]	Z [auth E]	DECANE C₁₀ H₂₂ DIOQZVSQGTUSAI-UHFFFAOYSA-N		Interactions Focus chain Z [auth E] Interactions & Density Focus chain Z [auth E]
ABU (Subject of Investigation/LOI) Query on ABU Download Ideal Coordinates CCD File SDF format, chain Q [auth A] SDF format, chain AA [auth E] MOL2 format, chain Q [auth A] MOL2 format, chain AA [auth E] mmCIF format, chain Q [auth A] mmCIF format, chain AA [auth E]	AA [auth E], Q [auth A]	GAMMA-AMINO-BUTANOIC ACID C₄ H₉ N O₂ BTCSSZJGUNDROE-UHFFFAOYSA-N		Interactions Focus chain AA [auth E] Focus chain Q [auth A] Interactions & Density Focus chain AA [auth E] Focus chain Q [auth A]
HEX Query on HEX Download Ideal Coordinates CCD File SDF format, chain X [auth D] SDF format, chain W [auth D] SDF format, chain U [auth B] SDF format, chain T [auth B] SDF format, chain S [auth B] SDF format, chain CA [auth E] SDF format, chain BA [auth E] MOL2 format, chain X [auth D] MOL2 format, chain W [auth D] MOL2 format, chain U [auth B] MOL2 format, chain T [auth B] MOL2 format, chain S [auth B] MOL2 format, chain CA [auth E] MOL2 format, chain BA [auth E] mmCIF format, chain X [auth D] mmCIF format, chain W [auth D] mmCIF format, chain U [auth B] mmCIF format, chain T [auth B] mmCIF format, chain S [auth B] mmCIF format, chain CA [auth E] mmCIF format, chain BA [auth E]	BA [auth E] CA [auth E] S [auth B] T [auth B] U [auth B] BA [auth E], CA [auth E], S [auth B], T [auth B], U [auth B], W [auth D], X [auth D]	HEXANE C₆ H₁₄ VLKZOEOYAKHREP-UHFFFAOYSA-N		Interactions Focus chain BA [auth E] Focus chain CA [auth E] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain W [auth D] Focus chain X [auth D] Interactions & Density Focus chain BA [auth E] Focus chain CA [auth E] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain W [auth D] Focus chain X [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain Y [auth D] SDF format, chain R [auth A] SDF format, chain HA [auth L] MOL2 format, chain Y [auth D] MOL2 format, chain R [auth A] MOL2 format, chain HA [auth L] mmCIF format, chain Y [auth D] mmCIF format, chain R [auth A] mmCIF format, chain HA [auth L]	HA [auth L], R [auth A], Y [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain HA [auth L] Focus chain R [auth A] Focus chain Y [auth D] Interactions & Density Focus chain HA [auth L] Focus chain R [auth A] Focus chain Y [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
P1L Query on P1L	E [auth C]	L-PEPTIDE LINKING	C₁₉ H₃₇ N O₃ S		CYS

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	19.2
RECONSTRUCTION	RELION	3.1

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-07-02

Deposition Author(s):

Kasaragod, V.B.

Aricescu, A.R.

Funding Organization	Location	Grant Number
Medical Research Council (MRC, United Kingdom)	United Kingdom	MC_UP_1201/15
European Molecular Biology Organization (EMBO)	European Union	ALTF137-2019
H2020 Marie Curie Actions of the European Commission	European Union	GABAARComp-897707
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