9FAK | pdb_00009fak

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 (StateD2)

PDB DOI: https://doi.org/10.2210/pdb9FAK/pdb
EM Map EMD-50274: 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), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), H2020 Marie Curie Actions of the European Commission, 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 (StateD2)

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

To be published.

Macromolecule Content

Total Structure Weight: 404.29 kDa
Atom Count: 19,569
Modeled Residue Count: 2,222
Deposited Residue Count: 3,417
Unique protein chains: 6

Macromolecules

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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P18507
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain C	Go to GlyGen: P18507-2
Sequence Annotations Expand
Reference Sequence

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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8NFZ4
Sequence Annotations Expand
Reference Sequence

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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q7Z7J7
Sequence Annotations Expand
Reference Sequence

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| 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

Oligosaccharides

Help

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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	D 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	D 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	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	M [auth K]	2		N-Glycosylation	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	D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)-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]	7		N-Glycosylation	Interactions Focus chain N [auth M] Interactions & Density Focus chain N [auth M]
Glycosylation Resources
GlyTouCan: G23799GS GlyCosmos: G23799GS GlyGen: G23799GS

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

View more in-depth experimental data

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
Medical Research Council (MRC, United Kingdom)	United Kingdom	MR/L009609/1
Medical Research Council (MRC, United Kingdom)	United Kingdom	MC_EX_MR/T046279/1
European Molecular Biology Organization (EMBO)	European Union	ALTF137-2019
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	1R01-GM135550
H2020 Marie Curie Actions of the European Commission	European Union	GABAARComp-897707
National Science Foundation (NSF, United States)	United States	NeuroNex 2014862

Revision History (Full details and data files)

Version 1.0: 2025-07-02
Type: Initial release

9FAK | pdb_00009fak

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 (StateD2)

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 (StateD2)

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Glycosylation

Sequence Annotations

Expand

Entity ID: 2

UniProt & NIH Common Fund Data Resources

Entity Groups

Glycosylation

Sequence Annotations

Expand

Entity ID: 3

UniProt & NIH Common Fund Data Resources

Entity Groups

Glycosylation

Sequence Annotations

Expand

Entity ID: 4

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Entity ID: 5

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Entity ID: 6

Oligosaccharides

Entity ID: 7

Glycosylation Resources

Entity ID: 8

Glycosylation Resources

Entity ID: 9

Glycosylation Resources

Entity ID: 10

Glycosylation Resources

Entity ID: 11

Glycosylation Resources

Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Entry History

Deposition Data

Revision History (Full details and data files)