9H9E | pdb_00009h9e

Cryo-EM structure of the human GABAA receptor alpha1 subunit in complex with the assembly factor NACHO/TMEM35A


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Mechanism of NACHO-mediated assembly of pentameric ligand-gated ion channels.

Hooda, Y.Sente, A.Judy, R.M.Smalinskaite, L.Chew, S.P.Naydenova, K.Malinauskas, T.Hardwick, S.W.Chirgadze, D.Y.Aricescu, A.R.Hegde, R.S.

(2024) bioRxiv 

  • DOI: https://doi.org/10.1101/2024.10.28.620708
  • Primary Citation of Related Structures:  
    9H9E

  • PubMed Abstract: 

    Pentameric ligand-gated ion channels (pLGICs) are cell surface receptors of crucial importance for animal physiology 1-4 . This diverse protein family mediates the ionotropic signals triggered by major neurotransmitters and includes γ-aminobutyric acid receptors (GABA A Rs) and acetylcholine receptors (nAChRs). Receptor function is fine-tuned by a myriad of endogenous and pharmacological modulators 3 . A functional pLGIC is built from five homologous, sometimes identical, subunits, each containing a β-scaffold extracellular domain (ECD), a four-helix transmembrane domain (TMD) and intracellular loops of variable length. Although considerable progress has been made in understanding pLGICs in structural and functional terms, the molecular mechanisms that enable their assembly at the endoplasmic reticulum (ER) 5 in a vast range of potential subunit configurations 6 remain unknown. Here, we identified candidate pLGICs assembly factors selectively associated with an unassembled GABA A R subunit. Focusing on one of the candidates, we determined the cryo-EM structure of an assembly intermediate containing two α1 subunits of GABA A R each bound to an ER-resident membrane protein NACHO. The structure showed how NACHO shields the principal (+) transmembrane interface of α1 subunits containing an immature extracellular conformation. Crosslinking and structure-prediction revealed an adjacent surface on NACHO for β2 subunit interactions to guide stepwise oligimerisation. Mutations of either subunit-interacting surface on NACHO also impaired the formation of homopentameric α7 nAChRs, pointing to a generic framework for pLGIC assembly. Our work provides the foundation for understanding the regulatory principles underlying pLGIC structural diversity.


  • Organizational Affiliation
    • MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, United Kingdom.

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
484Homo sapiensMutation(s): 0 
Gene Names: GABRA1
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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14867
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P14867-1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Novel acetylcholine receptor chaperone
B, C
187Homo sapiensMutation(s): 0 
Gene Names: TMEM35A
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q53FP2 (Homo sapiens)
Explore Q53FP2 
Go to UniProtKB:  Q53FP2
PHAROS:  Q53FP2
GTEx:  ENSG00000126950 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ53FP2
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseE [auth a],
F [auth d]
5N-Glycosylation
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PC7
Query on PC7

Download Ideal Coordinates CCD File 
H [auth A],
L [auth D]
(7S)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE
C42 H85 N O8 P
PZNPLUBHRSSFHT-FAIXQHPJSA-O
PGT
Query on PGT

Download Ideal Coordinates CCD File 
I [auth A],
M [auth D]
(1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
C40 H79 O10 P
KBPVYRBBONZJHF-AMAPPZPBSA-N
PX6
Query on PX6

Download Ideal Coordinates CCD File 
G [auth A],
K [auth D]
1,2-DIPALMITOYL-SN-GLYCERO-3-PHOSPHATE
C35 H68 O8 P
PORPENFLTBBHSG-MGBGTMOVSA-M
CLR
Query on CLR

Download Ideal Coordinates CCD File 
J [auth A],
N [auth D]
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC3.3.2
MODEL REFINEMENTPHENIXdev-5430-0000
MODEL REFINEMENTPHENIX1.19.2
MODEL REFINEMENTREFMAC5.8.0258
MODEL REFINEMENTServalcat

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United KingdomMC_UP_ A022_1007
Medical Research Council (MRC, United Kingdom)United KingdomMC_UP_1201/15
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1R01GM135550-01
Medical Research Council (MRC, United Kingdom)United KingdomMC_EX_MR/T046279/1
National Science Foundation (NSF, United States)United States2014862

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-04
    Type: Initial release