9FAJ | pdb_00009faj

CryoEM structure of human full-length alpha1beta3gamma2 GABA(A) receptor in complex with GARLH4, the TMD of Neuroligin2, GABA and Megabody38, in a desensitised state (StateD1)

PDB DOI: https://doi.org/10.2210/pdb9FAJ/pdb
EM Map EMD-50273: 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: 2.60 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) receptor in complex with GARLH4, the TMD of Neuroligin2, GABA and Megabody38, in a desensitised state (StateD1)

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

To be published.

Macromolecule Content

Total Structure Weight: 404.38 kDa
Atom Count: 19,645
Modeled Residue Count: 2,222
Deposited Residue Count: 3,417
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, 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
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A Focus chain D	Go to GlyGen: P14867-1
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Gamma-aminobutyric acid receptor subunit beta-3	B, 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 E	Go to GlyGen: P28472-1
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform 2 of Gamma-aminobutyric acid receptor subunit gamma-2	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
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

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
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

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
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Megabody38	H [auth G], I [auth P]	539	Lama glama	Mutation(s): 0
UniProt
Find proteins for B5Z8H1 (Helicobacter pylori (strain G27)) Explore B5Z8H1 Go to UniProtKB: B5Z8H1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B5Z8H1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

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	J [auth F]	10		N-Glycosylation	Interactions Focus chain J [auth F] Interactions & Density Focus chain J [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	K [auth I], P [auth O]	3		N-Glycosylation	Interactions Focus chain K [auth I] Focus chain P [auth O] Interactions & Density Focus chain K [auth I] Focus chain P [auth O]
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	L [auth J], O [auth N]	6		N-Glycosylation	Interactions Focus chain L [auth J] Focus chain O [auth N] Interactions & Density Focus chain L [auth J] Focus chain O [auth N]
Glycosylation Resources
GlyTouCan: G09724ZC GlyCosmos: G09724ZC GlyGen: G09724ZC

Entity ID: 10
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	M [auth K]	2		N/A	Interactions Focus chain M [auth K] Interactions & Density Focus chain M [auth K]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 11
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	N [auth M]	6		N-Glycosylation	Interactions Focus chain N [auth M] Interactions & Density Focus chain N [auth M]
Glycosylation Resources
GlyTouCan: G56014GC GlyCosmos: G56014GC GlyGen: G56014GC

Small Molecules

Ligands 11 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGW Query on PGW Download Ideal Coordinates CCD File SDF format, chain IB [auth L] SDF format, chain KB [auth L] SDF format, chain R [auth A] SDF format, chain SA [auth D] SDF format, chain BB [auth E] MOL2 format, chain IB [auth L] MOL2 format, chain KB [auth L] MOL2 format, chain R [auth A] MOL2 format, chain SA [auth D] MOL2 format, chain BB [auth E] mmCIF format, chain IB [auth L] mmCIF format, chain KB [auth L] mmCIF format, chain R [auth A] mmCIF format, chain SA [auth D] mmCIF format, chain BB [auth E]	BB [auth E], IB [auth L], KB [auth L], R [auth A], SA [auth D]	(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 BB [auth E] Focus chain IB [auth L] Focus chain KB [auth L] Focus chain R [auth A] Focus chain SA [auth D] Interactions & Density Focus chain BB [auth E] Focus chain IB [auth L] Focus chain KB [auth L] Focus chain R [auth A] Focus chain SA [auth D]
PIO Query on PIO Download Ideal Coordinates CCD File SDF format, chain Q [auth A] SDF format, chain QA [auth D] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth D] mmCIF format, chain Q [auth A] mmCIF format, chain QA [auth D]	Q [auth A], QA [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 Q [auth A] Focus chain QA [auth D] Interactions & Density Focus chain Q [auth A] Focus chain QA [auth D]
PX2 Query on PX2 Download Ideal Coordinates CCD File SDF format, chain IA [auth C] SDF format, chain V [auth A] SDF format, chain YA [auth E] SDF format, chain Z [auth B] SDF format, chain WA [auth D] MOL2 format, chain IA [auth C] MOL2 format, chain V [auth A] MOL2 format, chain YA [auth E] MOL2 format, chain Z [auth B] MOL2 format, chain WA [auth D] mmCIF format, chain IA [auth C] mmCIF format, chain V [auth A] mmCIF format, chain YA [auth E] mmCIF format, chain Z [auth B] mmCIF format, chain WA [auth D]	IA [auth C], V [auth A], WA [auth D], YA [auth E], Z [auth B]	1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE C₂₇ H₅₂ O₈ P OKLASJZQBDJAPH-RUZDIDTESA-M		Interactions Focus chain IA [auth C] Focus chain V [auth A] Focus chain WA [auth D] Focus chain YA [auth E] Focus chain Z [auth B] Interactions & Density Focus chain IA [auth C] Focus chain V [auth A] Focus chain WA [auth D] Focus chain YA [auth E] Focus chain Z [auth B]
CLR (Subject of Investigation/LOI) Query on CLR Download Ideal Coordinates CCD File SDF format, chain OA [auth C] MOL2 format, chain OA [auth C] mmCIF format, chain OA [auth C]	OA [auth C]	CHOLESTEROL C₂₇ H₄₆ O HVYWMOMLDIMFJA-DPAQBDIFSA-N		Interactions Focus chain OA [auth C] Interactions & Density Focus chain OA [auth C]
OLC Query on OLC Download Ideal Coordinates CCD File SDF format, chain KA [auth C] MOL2 format, chain KA [auth C] mmCIF format, chain KA [auth C]	KA [auth C]	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C₂₁ H₄₀ O₄ RZRNAYUHWVFMIP-GDCKJWNLSA-N		Interactions Focus chain KA [auth C] Interactions & Density Focus chain KA [auth C]
PLM Query on PLM Download Ideal Coordinates CCD File SDF format, chain HA [auth C] SDF format, chain NA [auth C] SDF format, chain MA [auth C] SDF format, chain LA [auth C] SDF format, chain DB [auth E] MOL2 format, chain HA [auth C] MOL2 format, chain NA [auth C] MOL2 format, chain MA [auth C] MOL2 format, chain LA [auth C] MOL2 format, chain DB [auth E] mmCIF format, chain HA [auth C] mmCIF format, chain NA [auth C] mmCIF format, chain MA [auth C] mmCIF format, chain LA [auth C] mmCIF format, chain DB [auth E]	DB [auth E], HA [auth C], LA [auth C], MA [auth C], NA [auth C]	PALMITIC ACID C₁₆ H₃₂ O₂ IPCSVZSSVZVIGE-UHFFFAOYSA-N		Interactions Focus chain DB [auth E] Focus chain HA [auth C] Focus chain LA [auth C] Focus chain MA [auth C] Focus chain NA [auth C] Interactions & Density Focus chain DB [auth E] Focus chain HA [auth C] Focus chain LA [auth C] Focus chain MA [auth C] Focus chain NA [auth C]
R16 Query on R16 Download Ideal Coordinates CCD File SDF format, chain EA [auth B] SDF format, chain ZA [auth E] SDF format, chain EB [auth E] SDF format, chain AA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain ZA [auth E] MOL2 format, chain EB [auth E] MOL2 format, chain AA [auth B] mmCIF format, chain EA [auth B] mmCIF format, chain ZA [auth E] mmCIF format, chain EB [auth E] mmCIF format, chain AA [auth B]	AA [auth B], EA [auth B], EB [auth E], ZA [auth E]	HEXADECANE C₁₆ H₃₄ DCAYPVUWAIABOU-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain EA [auth B] Focus chain EB [auth E] Focus chain ZA [auth E] Interactions & Density Focus chain AA [auth B] Focus chain EA [auth B] Focus chain EB [auth E] Focus chain ZA [auth E]
D10 Query on D10 Download Ideal Coordinates CCD File SDF format, chain BA [auth B] SDF format, chain FB [auth E] SDF format, chain JA [auth C] SDF format, chain JB [auth L] SDF format, chain T [auth A] SDF format, chain U [auth A] SDF format, chain UA [auth D] SDF format, chain X [auth A] SDF format, chain VA [auth D] SDF format, chain S [auth A] SDF format, chain GA [auth B] SDF format, chain AB [auth E] MOL2 format, chain BA [auth B] MOL2 format, chain FB [auth E] MOL2 format, chain JA [auth C] MOL2 format, chain JB [auth L] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain UA [auth D] MOL2 format, chain X [auth A] MOL2 format, chain VA [auth D] MOL2 format, chain S [auth A] MOL2 format, chain GA [auth B] MOL2 format, chain AB [auth E] mmCIF format, chain BA [auth B] mmCIF format, chain FB [auth E] mmCIF format, chain JA [auth C] mmCIF format, chain JB [auth L] mmCIF format, chain T [auth A] mmCIF format, chain U [auth A] mmCIF format, chain UA [auth D] mmCIF format, chain X [auth A] mmCIF format, chain VA [auth D] mmCIF format, chain S [auth A] mmCIF format, chain GA [auth B] mmCIF format, chain AB [auth E]	AB [auth E] BA [auth B] FB [auth E] GA [auth B] JA [auth C] AB [auth E], BA [auth B], FB [auth E], GA [auth B], JA [auth C], JB [auth L], S [auth A], T [auth A], U [auth A], UA [auth D], VA [auth D], X [auth A]	DECANE C₁₀ H₂₂ DIOQZVSQGTUSAI-UHFFFAOYSA-N		Interactions Focus chain AB [auth E] Focus chain BA [auth B] Focus chain FB [auth E] Focus chain GA [auth B] Focus chain JA [auth C] Focus chain JB [auth L] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain UA [auth D] Focus chain VA [auth D] Focus chain X [auth A] Interactions & Density Focus chain AB [auth E] Focus chain BA [auth B] Focus chain FB [auth E] Focus chain GA [auth B] Focus chain JA [auth C] Focus chain JB [auth L] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain UA [auth D] Focus chain VA [auth D] Focus chain X [auth A]
ABU (Subject of Investigation/LOI) Query on ABU Download Ideal Coordinates CCD File SDF format, chain W [auth A] SDF format, chain HB [auth E] MOL2 format, chain W [auth A] MOL2 format, chain HB [auth E] mmCIF format, chain W [auth A] mmCIF format, chain HB [auth E]	HB [auth E], W [auth A]	GAMMA-AMINO-BUTANOIC ACID C₄ H₉ N O₂ BTCSSZJGUNDROE-UHFFFAOYSA-N		Interactions Focus chain HB [auth E] Focus chain W [auth A] Interactions & Density Focus chain HB [auth E] Focus chain W [auth A]
HEX Query on HEX Download Ideal Coordinates CCD File SDF format, chain CB [auth E] SDF format, chain DA [auth B] SDF format, chain GB [auth E] SDF format, chain RA [auth D] SDF format, chain TA [auth D] SDF format, chain FA [auth B] SDF format, chain CA [auth B] MOL2 format, chain CB [auth E] MOL2 format, chain DA [auth B] MOL2 format, chain GB [auth E] MOL2 format, chain RA [auth D] MOL2 format, chain TA [auth D] MOL2 format, chain FA [auth B] MOL2 format, chain CA [auth B] mmCIF format, chain CB [auth E] mmCIF format, chain DA [auth B] mmCIF format, chain GB [auth E] mmCIF format, chain RA [auth D] mmCIF format, chain TA [auth D] mmCIF format, chain FA [auth B] mmCIF format, chain CA [auth B]	CA [auth B] CB [auth E] DA [auth B] FA [auth B] GB [auth E] CA [auth B], CB [auth E], DA [auth B], FA [auth B], GB [auth E], RA [auth D], TA [auth D]	HEXANE C₆ H₁₄ VLKZOEOYAKHREP-UHFFFAOYSA-N		Interactions Focus chain CA [auth B] Focus chain CB [auth E] Focus chain DA [auth B] Focus chain FA [auth B] Focus chain GB [auth E] Focus chain RA [auth D] Focus chain TA [auth D] Interactions & Density Focus chain CA [auth B] Focus chain CB [auth E] Focus chain DA [auth B] Focus chain FA [auth B] Focus chain GB [auth E] Focus chain RA [auth D] Focus chain TA [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain LB [auth L] SDF format, chain XA [auth D] SDF format, chain Y [auth A] SDF format, chain PA [auth C] MOL2 format, chain LB [auth L] MOL2 format, chain XA [auth D] MOL2 format, chain Y [auth A] MOL2 format, chain PA [auth C] mmCIF format, chain LB [auth L] mmCIF format, chain XA [auth D] mmCIF format, chain Y [auth A] mmCIF format, chain PA [auth C]	LB [auth L], PA [auth C], XA [auth D], Y [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain LB [auth L] Focus chain PA [auth C] Focus chain XA [auth D] Focus chain Y [auth A] Interactions & Density Focus chain LB [auth L] Focus chain PA [auth C] Focus chain XA [auth D] Focus chain Y [auth A]

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

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.60 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