6A96 | pdb_00006a96

Cryo-EM structure of the human alpha5beta3 GABAA receptor in complex with GABA and Nb25

• PDB DOI: https://doi.org/10.2210/pdb6A96/pdb
• EM Map EMD-6998: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Lama glama, Homo sapiens
• Expression System: Escherichia coli, Homo sapiens
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMD


• Deposited: 2018-07-11 Released: 2018-10-03 
• Deposition Author(s): Liu, S., Xu, L., Guan, F., Liu, Y.T., Cui, Y., Zhang, Q., Bi, G.Q., Zhou, Z.H., Zhang, X., Ye, S.
• Funding Organization(s): Ministry of Science and Technology (China), National Natural Science Foundation of China, National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI), National Science Foundation (China)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.51 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structure of the human alpha 5 beta 3 GABAAreceptor.

Liu, S., Xu, L., Guan, F., Liu, Y.T., Cui, Y., Zhang, Q., Zheng, X., Bi, G.Q., Zhou, Z.H., Zhang, X., Ye, S.

(2018) Cell Res 28: 958-961

• PubMed: 30140029 
• DOI: https://doi.org/10.1038/s41422-018-0077-8
• Primary Citation of Related Structures:  
  6A96

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Organizational Affiliation: 
• Life Sciences Institute and School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310058, P. R. China.
Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, 310058, P. R. China.
Center for Integrative Imaging, Hefei National Laboratory for Physical Sciences at the Microscale, and School of Life Sciences, University of Science and Technology of China (USTC), Hefei, Anhui, 230026, P. R. China.
School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026, P. R. China.
CAS Key Laboratory of Brain Function and Disease, University of Science and Technology of China, Hefei, Anhui, 230026, P. R. China.
Electron Imaging Center for Nanomachines, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
Department of Biophysics, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310058, P. R. China.
Center of Cryo Electron Microscopy, Zhejiang University, Hangzhou, Zhejiang, 310058, P. R. China.
CAS Center for Excellence in Brain Science and Intelligence Technology, University of Science and Technology of China, Hefei, Anhui, 230026, P. R. China.
Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, 90095, USA. [e-mail].
California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA, 90095, USA. [e-mail].
Department of Biophysics, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310058, P. R. China. [e-mail].
Center of Cryo Electron Microscopy, Zhejiang University, Hangzhou, Zhejiang, 310058, P. R. China. [e-mail].
Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, 310058, P. R. China. [e-mail].
School of Life Sciences, Tianjin University, 92 Weijin Road, Nankai District, Tianjin, 300072, P. R. China. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 8-mer - A4B3C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 8-mer - A5B3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 261.76 kDa 
• Atom Count: 17,049 
• Modeled Residue Count: 2,043 
• Deposited Residue Count: 2,231 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nb25	A [auth K], B [auth L], C [auth O]	125	Lama glama	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Gamma-aminobutyric acid receptor subunit beta-3,Gamma-aminobutyric acid receptor subunit beta-3	D [auth B], F [auth E], G [auth C], H [auth D]	366	Homo sapiens	Mutation(s): 0  Gene Names: GABRB3 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P28472 (Homo sapiens) Explore P28472  Go to UniProtKB:  P28472
PHAROS:  P28472 GTEx:  ENSG00000166206
Glycosylation
Glycosylation Sites: 2		Go to GlyGen: P28472-1

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Gamma-aminobutyric acid receptor subunit alpha-5,Gamma-aminobutyric acid receptor subunit alpha-5	E [auth A]	392	Homo sapiens	Mutation(s): 0  Gene Names: GABRA5 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P31644 (Homo sapiens) Explore P31644  Go to UniProtKB:  P31644
PHAROS:  P31644 GTEx:  ENSG00000186297
Glycosylation
Glycosylation Sites: 2		Go to GlyGen: P31644-1

Oligosaccharides

Help

Entity ID: 4
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	I [auth F], M [auth J], O [auth N], Q	6		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G09724ZC GlyCosmos:  G09724ZC GlyGen:  G09724ZC

Entity ID: 5
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 G], N [auth M], P, R	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
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 H]	5		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22768VO GlyCosmos:  G22768VO GlyGen:  G22768VO

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	L [auth I]	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ABU (Subject of Investigation/LOI)	S [auth B]	GAMMA-AMINO-BUTANOIC ACID C4 H9 N O2 BTCSSZJGUNDROE-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
ABU	BindingDB:  6A96	Ki: min: 8.7, max: 22.9 (nM) from 2 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: 3.51 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	0.55

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-10-03 
Deposition Author(s): Liu, S., Xu, L., Guan, F., Liu, Y.T., Cui, Y., Zhang, Q., Bi, G.Q., Zhou, Z.H., Zhang, X., Ye, S.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (China)	China	2016YFA0500404
Ministry of Science and Technology (China)	China	2014CB910300
Ministry of Science and Technology (China)	China	2016YFA0501102
National Natural Science Foundation of China	China	31630030
National Natural Science Foundation of China	China	31525001
National Natural Science Foundation of China	China	31430019
National Natural Science Foundation of China	China	31600606
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	GM071940
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	S10RR23057
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	S10OD018111
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	U24GM116792
National Science Foundation (China)	China	DBI-1338135
National Science Foundation (China)	China	DMR-1548924

Revision History  

• Version 1.0: 2018-10-03
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2022-03-23
  Changes: Author supporting evidence, Database references, Derived calculations, Structure summary
• Version 3.0: 2023-11-15
  Changes: Advisory, Atomic model, Data collection
• Version 4.0: 2025-09-17
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary