6X3V

Human GABAA receptor alpha1-beta2-gamma2 subtype in complex with GABA plus etomidate

• PDB DOI: https://doi.org/10.2210/pdb6X3V/pdb
• EM Map EMD-22034: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens, Mus musculus
• Expression System: Homo sapiens
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMDmpstruc


• Deposited: 2020-05-21 Released: 2020-09-09 
• Deposition Author(s): Kim, J.J., Gharpure, A., Teng, J., Zhuang, Y., Howard, R.J., Zhu, S., Noviello, C.M., Walsh, R.M., Lindahl, E., Hibbs, R.E.
• Funding Organization(s): National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA), National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS), Welch Foundation, American Heart Association

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Experimental Data Snapshot

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 9-mer - A2B2C2D2E1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 9-mer - A5B4 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - C2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 365.09 kDa 
• Atom Count: 17,426 
• Modelled Residue Count: 2,121 
• Deposited Residue Count: 3,195 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gamma-aminobutyric acid receptor subunit beta-2	A, C	364	Homo sapiens	Mutation(s): 0  Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P47870 (Homo sapiens) Explore P47870  Go to UniProtKB:  P47870
PHAROS:  P47870 GTEx:  ENSG00000145864

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Gamma-aminobutyric acid receptor subunit alpha-1	B, D	358	Homo sapiens	Mutation(s): 0  Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P14867 (Homo sapiens) Explore P14867  Go to UniProtKB:  P14867
PHAROS:  P14867 GTEx:  ENSG00000022355

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Gamma-aminobutyric acid receptor subunit gamma-2	E	417	Homo sapiens	Mutation(s): 0  Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P18507 (Homo sapiens) Explore P18507  Go to UniProtKB:  P18507
PHAROS:  P18507 GTEx:  ENSG00000113327

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Kappa Fab Light Chain	F [auth I], H [auth L]	213	Mus musculus	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
IgG2b Fab Heavy Chain	G [auth J], I [auth K]	454	Mus musculus	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 6
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 F], L [auth H], M	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

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	K [auth G]	10		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G40702WU GlyCosmos:  G40702WU GlyGen:  G40702WU

Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	N	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
V8D (Subject of Investigation/LOI)	Q [auth A], T [auth C]	Etomidate C14 H16 N2 O2 NPUKDXXFDDZOKR-LLVKDONJSA-N
NAG	O [auth A], R [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
ABU (Subject of Investigation/LOI)	P [auth A], S [auth C]	GAMMA-AMINO-BUTANOIC ACID C4 H9 N O2 BTCSSZJGUNDROE-UHFFFAOYSA-N

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
RECONSTRUCTION	RELION
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-09-09 
Deposition Author(s): Kim, J.J., Gharpure, A., Teng, J., Zhuang, Y., Howard, R.J., Zhu, S., Noviello, C.M., Walsh, R.M., Lindahl, E., Hibbs, R.E.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)	United States	DA037492
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)	United States	DA042072
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	United States	NS095899
Welch Foundation	United States	I-1812
American Heart Association	United States	20POST35200127

Revision History  

• Version 1.0: 2020-09-09
  Type: Initial release
  
• Version 1.1: 2020-09-16
  Changes: Database references
• Version 1.2: 2020-09-23
  Changes: Database references
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Database references
• Version 3.0: 2024-01-31
  Changes: Atomic model, Data collection, Derived calculations, Structure summary