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 
- 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
Experimental Data Snapshot
- Method: ELECTRON MICROSCOPY
- Resolution: 3.50 Å
- Aggregation State: PARTICLE 
- Reconstruction Method: SINGLE PARTICLE 
wwPDB Validation   3D Report Full Report
This is version 3.0 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Gamma-aminobutyric acid receptor subunit beta-2 | 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 Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P47870 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Gamma-aminobutyric acid receptor subunit alpha-1 | 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 Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P14867 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Gamma-aminobutyric acid receptor subunit gamma-2 | 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 Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P18507 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 4 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Kappa Fab Light Chain | F [auth I], H [auth L] | 213 | Mus musculus | Mutation(s): 0  | |
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 5 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
IgG2b Fab Heavy Chain | G [auth J], I [auth K] | 454 | Mus musculus | Mutation(s): 0  | |
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
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 | |||||
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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 |
Small Molecules
Ligands 3 Unique | |||||
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ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
V8D (Subject of Investigation/LOI) Query on V8D | Q [auth A], T [auth C] | Etomidate C14 H16 N2 O2 NPUKDXXFDDZOKR-LLVKDONJSA-N | |||
NAG Query on 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) Query on ABU | 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 
Task | Software Package | Version |
---|---|---|
RECONSTRUCTION | RELION | |
MODEL REFINEMENT | PHENIX |
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.
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 (Full details and data files)
- 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