6A96

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)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.51 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.

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 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41422-018-0077-8
Primary Citation of Related Structures:
6A96

Organizational Affiliation

Life Sciences Institute and School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310058, P. R. China.

Macromolecule Content

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

Macromolecules

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(by identity cutoff) | 3D Structure

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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P28472
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain D [auth B] Focus chain F [auth E] Focus chain G [auth C] Focus chain H [auth D]	Go to GlyGen: P28472-1
Sequence Annotations Expand
Reference Sequence LOADING

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P31644
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain E [auth A]	Go to GlyGen: P31644-1
Sequence Annotations Expand
Reference Sequence LOADING

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	Interactions Focus chain I [auth F] Focus chain M [auth J] Focus chain O [auth N] Focus chain Q Interactions & Density Focus chain I [auth F] Focus chain M [auth J] Focus chain O [auth N] Focus chain Q
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	Interactions Focus chain J [auth G] Focus chain N [auth M] Focus chain P Focus chain R Interactions & Density Focus chain J [auth G] Focus chain N [auth M] Focus chain P Focus chain R
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	Interactions Focus chain K [auth H] Interactions & Density Focus chain K [auth H]
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	Interactions Focus chain L [auth I] Interactions & Density Focus chain L [auth I]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ABU (Subject of Investigation/LOI) Query on ABU Download Ideal Coordinates CCD File SDF format, chain S [auth B] MOL2 format, chain S [auth B] mmCIF format, chain S [auth B]	S [auth B]	GAMMA-AMINO-BUTANOIC ACID C₄ H₉ N O₂ BTCSSZJGUNDROE-UHFFFAOYSA-N		Interactions Focus chain S [auth B] Interactions & Density Focus chain S [auth B]

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

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2018-10-03

Deposition Author(s):

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 (Full details and data files)

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