Movatterモバイル変換


[0]ホーム

URL:


RCSB PDB
235,183 Structures from the PDB
1,068,577 Computed Structure Models (CSM)
  • PDB-101
  • wwPDB
  • EMDataResource
  • NAKB: Nucleic Acid Knowledgebase
  • wwPDB Foundation
  • PDB-IHM Logo

 6DW1|pdb_00006dw1

Cryo-EM structure of the benzodiazepine-sensitive alpha1beta1gamma2S tri-heteromeric GABAA receptor in complex with GABA (ECD map)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation  3D Report Full Report


This is version 3.1 of the entry. See complete history


Literature

Cryo-EM structure of the benzodiazepine-sensitive alpha 1 beta 1 gamma 2S tri-heteromeric GABAAreceptor in complex with GABA.

Phulera, S.Zhu, H.Yu, J.Claxton, D.P.Yoder, N.Yoshioka, C.Gouaux, E.

(2018) Elife 7

  • PubMed30044221 Search on PubMedSearch on PubMed Central
  • DOI: https://doi.org/10.7554/eLife.39383
  • Primary Citation of Related Structures:  
    6DW0,6DW1

  • PubMed Abstract: 

    Fast inhibitory neurotransmission in the mammalian nervous system is largely mediated by GABAA receptors, chloride-selective members of the superfamily of pentameric Cys-loop receptors. Native GABAA receptors are heteromeric assemblies sensitive to many important drugs, from sedatives to anesthetics and anticonvulsant agents, with mutant forms of GABAA receptors implicated in multiple neurological diseases. Despite the profound importance of heteromeric GABAA receptors in neuroscience and medicine, they have proven recalcitrant to structure determination. Here we present the structure of a tri-heteromeric α1β1γ2SEM GABAA receptor in complex with GABA, determined by single particle cryo-EM at 3.1-3.8 Å resolution, elucidating molecular principles of receptor assembly and agonist binding. Remarkable N-linked glycosylation on the α1 subunit occludes the extracellular vestibule of the ion channel and is poised to modulate receptor assembly and perhaps ion channel gating. Our work provides a pathway to structural studies of heteromeric GABAA receptors and a framework for rational design of novel therapeutic agents.


  • Organizational Affiliation

    Vollum Institute, Oregon Health and Science University, Portland, United States.

Biological Assembly 1  

 Explore in 3DStructure |Sequence Annotations |Electron Density |Validation Report |Ligand Interaction (ABU) |Predict Membrane 


Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A2B2C1 
Pseudo Symmetry: Cyclic - C5  (Explore in 3D)
Pseudo Stoichiometry: Homo 5-mer - A5 


Find Similar Assemblies

Biological assembly 1 assigned by authors and generated by PISA (software)


Biological Assembly Evidence: gel filtration
PreviousNext

Macromolecule Content

  • Total Structure Weight: 242.41 kDa 
  • Atom Count: 8,595 
  • Modelled Residue Count: 1,046 
  • Deposited Residue Count: 2,062 
  • Unique protein chains: 3

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Gamma-aminobutyric acid receptor subunit gamma-2A [auth D]490Rattus norvegicusMutation(s): 0 
Gene Names: Gabrg2
Membrane Entity: Yes 
UniProt
Find proteins for P18508 (Rattus norvegicus)
Explore P18508 
Go to UniProtKB:  P18508
Entity Groups 
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP18508
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Gamma-aminobutyric acid receptor subunit alpha-1,Gamma-aminobutyric acid receptor subunit alpha-1B [auth C],
C [auth A]
402Rattus norvegicusMutation(s): 0 
Gene Names: Gabra1Gabra-1
Membrane Entity: Yes 
UniProt
Find proteins for P62813 (Rattus norvegicus)
Explore P62813 
Go to UniProtKB:  P62813
Entity Groups 
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62813
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P62813-1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Gamma-aminobutyric acid receptor subunit beta-1,Gamma-aminobutyric acid receptor subunit beta-1D [auth E],
E [auth B]
384Rattus norvegicusMutation(s): 0 
Gene Names: Gabrb1Gabrb-1
Membrane Entity: Yes 
UniProt
Find proteins for P15431 (Rattus norvegicus)
Explore P15431 
Go to UniProtKB:  P15431
Entity Groups 
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15431
Glycosylation
Glycosylation Sites: 2Go to GlyGen: P15431-1
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
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
F
4N-Glycosylation
Glycosylation Resources
GlyTouCan:  G81315DD
GlyCosmos:  G81315DD
GlyGen:  G81315DD
Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[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
G
7N-Glycosylation
Glycosylation Resources
GlyTouCan:  G07617FP
GlyCosmos:  G07617FP
GlyGen:  G07617FP
Entity ID: 6
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
H, J
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 7
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
I, K
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
ABUBindingDB: 6DW1Ki: min: 8.7, max: 77.62 (nM) from 6 assay(s)
IC50: 22 (nM) from 1 assay(s)
EC50: min: 230, max: 8.00e+4 (nM) from 20 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.13
RECONSTRUCTIONRELION2.1

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM100400
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-08
    Type: Initial release
  • Version 1.1: 2019-11-20
    Changes: Author supporting evidence
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 3.0: 2023-11-15
    Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
  • Version 3.1: 2024-10-23
    Changes: Data collection, Structure summary
  • RCSB PDB is hosted by

  • The Rutgers Artificial Intelligence and Data Science Collaboratory logo
    Uiversity of California San Diego logoSan Diego Supercomputer Center logo
    University of California San Francisco Logo

RCSB PDB Core Operations are funded by theU.S. National Science Foundation (DBI-2321666), theUS Department of Energy (DE-SC0019749), and theNational Cancer Institute,National Institute of Allergy and Infectious Diseases, andNational Institute of General Medical Sciences of theNational Institutes of Health under grant R01GM157729.


[8]ページ先頭

©2009-2025 Movatter.jp