A Closed pore conformation of a Pentameic ligand-gated ion channel with additional N-terminal domain

Experimental Data Snapshot

  • Resolution: 3.55 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.197 

Starting Models: experimental
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Structural basis for allosteric transitions of a multidomain pentameric ligand-gated ion channel.

Hu, H.Howard, R.J.Bastolla, U.Lindahl, E.Delarue, M.

(2020) Proc Natl Acad Sci U S A 117: 13437-13446

  • DOI: https://doi.org/10.1073/pnas.1922701117
  • Primary Citation of Related Structures:  
    6V4A, 6V4B, 6V4S

  • PubMed Abstract: 

    Pentameric ligand-gated ion channels (pLGICs) are allosteric receptors that mediate rapid electrochemical signal transduction in the animal nervous system through the opening of an ion pore upon binding of neurotransmitters. Orthologs have been found and characterized in prokaryotes and they display highly similar structure-function relationships to eukaryotic pLGICs; however, they often encode greater architectural diversity involving additional amino-terminal domains (NTDs). Here we report structural, functional, and normal-mode analysis of two conformational states of a multidomain pLGIC, called DeCLIC, from a Desulfofustis deltaproteobacterium, including a periplasmic NTD fused to the conventional ligand-binding domain (LBD). X-ray structure determination revealed an NTD consisting of two jelly-roll domains interacting across each subunit interface. Binding of Ca 2+ at the LBD subunit interface was associated with a closed transmembrane pore, with resolved monovalent cations intracellular to the hydrophobic gate. Accordingly, DeCLIC-injected oocytes conducted currents only upon depletion of extracellular Ca 2+ ; these were insensitive to quaternary ammonium block. Furthermore, DeCLIC crystallized in the absence of Ca 2+ with a wide-open pore and remodeled periplasmic domains, including increased contacts between the NTD and classic LBD agonist-binding sites. Functional, structural, and dynamical properties of DeCLIC paralleled those of sTeLIC, a pLGIC from another symbiotic prokaryote. Based on these DeCLIC structures, we would reclassify the previous structure of bacterial ELIC (the first high-resolution structure of a pLGIC) as a "locally closed" conformation. Taken together, structures of DeCLIC in multiple conformations illustrate dramatic conformational state transitions and diverse regulatory mechanisms available to ion channels in pLGICs, particularly involving Ca 2+ modulation and periplasmic NTDs.

  • Organizational Affiliation

    Unité Dynamique Structurale des Macromolécules, Institut Pasteur, UMR 3528, CNRS, 75015 Paris, France.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Neur_chan_LBD domain-containing proteinA,
B [auth E],
C [auth D],
D [auth C],
E [auth B]
642Desulfofustis sp. PB-SRB1Mutation(s): 0 
Gene Names: N839_03575
Membrane Entity: Yes 
Find proteins for V4JF97 (Desulfofustis sp. PB-SRB1)
Explore V4JF97 
Go to UniProtKB:  V4JF97
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupV4JF97
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on LMT

Download Ideal Coordinates CCD File 
DA [auth B]
EA [auth B]
FA [auth B]
L [auth A]
O [auth E]
DA [auth B],
EA [auth B],
FA [auth B],
L [auth A],
O [auth E],
P [auth E],
Q [auth E],
T [auth D],
Y [auth C],
Z [auth C]
C24 H46 O11
Query on CA

Download Ideal Coordinates CCD File 
AA [auth B],
F [auth A],
G [auth A],
M [auth E],
U [auth C]
Query on CL

Download Ideal Coordinates CCD File 
CA [auth B],
K [auth A],
N [auth E],
S [auth D],
X [auth C]
Query on NA

Download Ideal Coordinates CCD File 
BA [auth B]
H [auth A]
I [auth A]
J [auth A]
R [auth D]
BA [auth B],
H [auth A],
I [auth A],
J [auth A],
R [auth D],
V [auth C],
W [auth C]
Experimental Data & Validation

Experimental Data

  • Resolution: 3.55 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.197 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 159.406α = 90
b = 337.254β = 90
c = 111.812γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-06-03
    Type: Initial release
  • Version 1.1: 2020-06-17
    Changes: Database references
  • Version 1.2: 2020-07-01
    Changes: Database references
  • Version 1.3: 2023-10-11
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description