5IUX

GLIC-V135C bimane labelled X-ray structure


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.237 (Depositor), 0.254 (DCC) 
  • R-Value Work: 
    0.203 (Depositor), 0.217 (DCC) 
  • R-Value Observed: 
    0.205 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted PC1Click on this verticalbar to view detailsBest fitted LMTClick on this verticalbar to view detailsBest fitted 6E3Click on this verticalbar to view details

This is version 1.4 of the entry. See complete history


Literature

Identification of a pre-active conformation of a pentameric channel receptor.

Menny, A.Lefebvre, S.N.Schmidpeter, P.A.Drege, E.Fourati, Z.Delarue, M.Edelstein, S.J.Nimigean, C.M.Joseph, D.Corringer, P.J.

(2017) Elife 6

  • DOI: https://doi.org/10.7554/eLife.23955
  • Primary Citation of Related Structures:  
    5IUX

  • PubMed Abstract: 

    Pentameric ligand-gated ion channels (pLGICs) mediate fast chemical signaling through global allosteric transitions. Despite the existence of several high-resolution structures of pLGICs, their dynamical properties remain elusive. Using the proton-gated channel GLIC, we engineered multiple fluorescent reporters, each incorporating a bimane and a tryptophan/tyrosine, whose close distance causes fluorescence quenching. We show that proton application causes a global compaction of the extracellular subunit interface, coupled to an outward motion of the M2-M3 loop near the channel gate. These movements are highly similar in lipid vesicles and detergent micelles. These reorganizations are essentially completed within 2 ms and occur without channel opening at low proton concentration, indicating that they report a pre-active intermediate state in the transition pathway toward activation. This provides a template to investigate the gating of eukaryotic neurotransmitter receptors, for which intermediate states also participate in activation.


  • Organizational Affiliation

    Channel Receptors Unit, Institut Pasteur, Paris, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Proton-gated ion channel
A, B, C, D, E
317Gloeobacter violaceus PCC 7421Mutation(s): 1 
Gene Names: glvIglr4197
Membrane Entity: Yes 
UniProt
Find proteins for Q7NDN8 (Gloeobacter violaceus (strain ATCC 29082 / PCC 7421))
Explore Q7NDN8 
Go to UniProtKB:  Q7NDN8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7NDN8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PC1
Query on PC1

Download Ideal Coordinates CCD File 
EA [auth D]
FA [auth D]
G [auth A]
GA [auth D]
H [auth A]
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H88 N O8 P
NRJAVPSFFCBXDT-HUESYALOSA-N
LMT
Query on LMT

Download Ideal Coordinates CCD File 
F [auth A]
K [auth A]
NA [auth E]
OA [auth E]
Q [auth B]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
6E3
Query on 6E3

Download Ideal Coordinates CCD File 
HA [auth D],
L [auth A]
2,3,5,6-tetramethyl-1H,7H-pyrazolo[1,2-a]pyrazole-1,7-dione
C10 H12 N2 O2
VWKNUUOGGLNRNZ-UHFFFAOYSA-N
BR
Query on BR

Download Ideal Coordinates CCD File 
AA [auth C],
IA [auth D],
M [auth A],
SA [auth E],
T [auth B]
BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
ACT
Query on ACT

Download Ideal Coordinates CCD File 
CA [auth C]
DA [auth C]
J [auth A]
KA [auth D]
LA [auth D]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
BA [auth C],
JA [auth D],
TA [auth E],
U [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.237 (Depositor), 0.254 (DCC) 
  • R-Value Work:  0.203 (Depositor), 0.217 (DCC) 
  • R-Value Observed: 0.205 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 182.034α = 90
b = 134.075β = 102.51
c = 159.945γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
SCALAdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted PC1Click on this verticalbar to view detailsBest fitted LMTClick on this verticalbar to view detailsBest fitted 6E3Click on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-29
    Type: Initial release
  • Version 1.1: 2018-01-31
    Changes: Database references
  • Version 1.2: 2018-05-09
    Changes: Data collection, Database references
  • Version 1.3: 2019-10-16
    Changes: Data collection
  • Version 1.4: 2024-11-20
    Changes: Data collection, Database references, Derived calculations, Structure summary