9EQG | pdb_00009eqg

CryoEM structure of human full-length alpha1beta3gamma2L GABA(A)R in complex with GABA and puerarin

  • Classification: MEMBRANE PROTEIN
  • Organism(s): Homo sapiens
  • Expression System: Homo sapiens
  • Mutation(s): No 

  • Deposited: 2024-03-21 Released: 2024-09-18 
  • Deposition Author(s): Kasaragod, V.B., Aricescu, A.R.
  • Funding Organization(s): Medical Research Council (MRC, United Kingdom), European Molecular Biology Organization (EMBO), H2020 Marie Curie Actions of the European Commission

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

A brain-to-gut signal controls intestinal fat absorption.

Lyu, Q.Xue, W.Liu, R.Ma, Q.Kasaragod, V.B.Sun, S.Li, Q.Chen, Y.Yuan, M.Yang, Y.Zhang, B.Nie, A.Jia, S.Shen, C.Gao, P.Rong, W.Yu, C.Bi, Y.Zhang, C.Nan, F.Ning, G.Rao, Z.Yang, X.Wang, J.Wang, W.

(2024) Nature 634: 936-943

  • DOI: https://doi.org/10.1038/s41586-024-07929-5
  • Primary Citation of Related Structures:  
    9EQG

  • PubMed Abstract: 

    Although fat is a crucial source of energy in diets, excessive intake leads to obesity. Fat absorption in the gut is prevailingly thought to occur organ-autonomously by diffusion 1-3 . Whether the process is controlled by the brain-to-gut axis, however, remains largely unknown. Here we demonstrate that the dorsal motor nucleus of vagus (DMV) plays a key part in this process. Inactivation of DMV neurons reduces intestinal fat absorption and consequently causes weight loss, whereas activation of the DMV increases fat absorption and weight gain. Notably, the inactivation of a subpopulation of DMV neurons that project to the jejunum shortens the length of microvilli, thereby reducing fat absorption. Moreover, we identify a natural compound, puerarin, that mimics the suppression of the DMV-vagus pathway, which in turn leads to reduced fat absorption. Photoaffinity chemical methods and cryogenic electron microscopy of the structure of a GABA A receptor-puerarin complex reveal that puerarin binds to an allosteric modulatory site. Notably, conditional Gabra1 knockout in the DMV largely abolishes puerarin-induced intestinal fat loss. In summary, we discover that suppression of the DMV-vagus-jejunum axis controls intestinal fat absorption by shortening the length of microvilli and illustrate the therapeutic potential of puerarin binding to GABRA1 in fat loss.


  • Organizational Affiliation
    • Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Gamma-aminobutyric acid receptor subunit alpha-1
A, D
464Homo sapiensMutation(s): 0 
Gene Names: GABRA1
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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14867
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P14867-1
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Gamma-aminobutyric acid receptor subunit beta-3
B, E
473Homo sapiensMutation(s): 0 
Gene Names: GABRB3
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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP28472
Glycosylation
Glycosylation Sites: 2Go to GlyGen: P28472-1
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Gamma-aminobutyric acid receptor subunit gamma-2495Homo sapiensMutation(s): 0 
Gene Names: GABRG2
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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP18507
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P18507-2
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D 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
F
10N-Glycosylation
Glycosylation Resources
GlyTouCan:  G40702WU
GlyCosmos:  G40702WU
GlyGen:  G40702WU
Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D 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
G, I, J
6N-Glycosylation
Glycosylation Resources
GlyTouCan:  G09724ZC
GlyCosmos:  G09724ZC
GlyGen:  G09724ZC
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, K
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Small Molecules
Ligands 11 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PT5
Query on PT5

Download Ideal Coordinates CCD File 
P [auth A],
QA [auth D]
[(2R)-1-octadecanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phospho ryl]oxy-propan-2-yl] (8Z)-icosa-5,8,11,14-tetraenoate
C47 H85 O19 P3
CNWINRVXAYPOMW-HJBQCNPJSA-N
PGW
Query on PGW

Download Ideal Coordinates CCD File 
L [auth A],
LA [auth D]
(1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate
C40 H77 O10 P
PAZGBAOHGQRCBP-HGWHEPCSSA-N
PX2
Query on PX2

Download Ideal Coordinates CCD File 
RA [auth D]1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE
C27 H52 O8 P
OKLASJZQBDJAPH-RUZDIDTESA-M
A1H6W (Subject of Investigation/LOI)
Query on A1H6W

Download Ideal Coordinates CCD File 
PA [auth D]Puerarin
C21 H20 O9
HKEAFJYKMMKDOR-VPRICQMDSA-N
PLM
Query on PLM

Download Ideal Coordinates CCD File 
DA [auth C],
MA [auth D],
U [auth A]
PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
R16
Query on R16

Download Ideal Coordinates CCD File 
JA [auth C],
Q [auth A],
TA [auth E],
W [auth B],
Y [auth B]
HEXADECANE
C16 H34
DCAYPVUWAIABOU-UHFFFAOYSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
HA [auth C]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
D10
Query on D10

Download Ideal Coordinates CCD File 
CA [auth C]
EA [auth C]
GA [auth C]
M [auth A]
N [auth A]
CA [auth C],
EA [auth C],
GA [auth C],
M [auth A],
N [auth A],
NA [auth D],
OA [auth D],
T [auth A],
UA [auth E],
WA [auth E],
X [auth B]
DECANE
C10 H22
DIOQZVSQGTUSAI-UHFFFAOYSA-N
ABU
Query on ABU

Download Ideal Coordinates CCD File 
AA [auth B],
XA [auth E]
GAMMA-AMINO-BUTANOIC ACID
C4 H9 N O2
BTCSSZJGUNDROE-UHFFFAOYSA-N
HEX
Query on HEX

Download Ideal Coordinates CCD File 
BA [auth B]
FA [auth C]
IA [auth C]
O [auth A]
R [auth A]
BA [auth B],
FA [auth C],
IA [auth C],
O [auth A],
R [auth A],
S [auth A],
VA [auth E],
YA [auth E],
Z [auth B],
ZA [auth E]
HEXANE
C6 H14
VLKZOEOYAKHREP-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
KA [auth C],
SA [auth D],
V [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19.2
RECONSTRUCTIONcryoSPARC4.40

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United KingdomMC_UP_1201/15
European Molecular Biology Organization (EMBO)European UnionALTF137-2019
H2020 Marie Curie Actions of the European CommissionEuropean UnionGABAARComp-897707

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-18
    Type: Initial release
  • Version 1.1: 2024-09-25
    Changes: Data collection, Database references
  • Version 1.2: 2024-10-23
    Changes: Data collection, Structure summary
  • Version 1.3: 2024-11-06
    Changes: Data collection, Database references