3UUB

The GLIC pentameric Ligand-Gated Ion Channel Loop2-21' mutant reduced in solution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.218 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

A locally closed conformation of a bacterial pentameric proton-gated ion channel.

Prevost, M.S.Sauguet, L.Nury, H.Van Renterghem, C.Huon, C.Poitevin, F.Baaden, M.Delarue, M.Corringer, P.J.

(2012) Nat Struct Mol Biol 19: 642-649

  • DOI: https://doi.org/10.1038/nsmb.2307
  • Primary Citation of Related Structures:  
    3TLS, 3TLT, 3TLU, 3TLV, 3TLW, 3UU3, 3UU4, 3UU5, 3UU6, 3UU8, 3UUB

  • PubMed Abstract: 

    Pentameric ligand-gated ion channels mediate signal transduction through conformational transitions between closed-pore and open-pore states. To stabilize a closed conformation of GLIC, a bacterial proton-gated homolog from Gloeobacter violaceus whose open structure is known, we separately generated either four cross-links or two single mutations. We found all six mutants to be in the same 'locally closed' conformation using X-ray crystallography, sharing most of the features of the open form but showing a locally closed pore as a result of a concerted bending of all of its M2 helices. The mutants adopt several variant conformations of the M2-M3 loop, and in all cases an interacting lipid that is observed in the open form disappears. A single cross-linked mutant is functional, according to electrophysiology, and the locally closed structure of this mutant indicates that it has an increased flexibility. Further cross-linking, accessibility and molecular dynamics data suggest that the locally closed form is a functionally relevant conformation that occurs during allosteric gating transitions.


  • Organizational Affiliation

    Institut Pasteur, Groupe Récepteurs-Canaux, Paris, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glr4197 protein
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J
321Gloeobacter violaceusMutation(s): 3 
Gene Names: glr4197
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 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PLC
Query on PLC

Download Ideal Coordinates CCD File 
BA [auth D]
CA [auth D]
DA [auth D]
DB [auth I]
EB [auth I]
BA [auth D],
CA [auth D],
DA [auth D],
DB [auth I],
EB [auth I],
FB [auth I],
GA [auth E],
HA [auth E],
HB [auth J],
IA [auth E],
IB [auth J],
JB [auth J],
K [auth A],
L [auth A],
LA [auth F],
M [auth A],
MA [auth F],
N [auth A],
NA [auth F],
R [auth B],
RA [auth G],
S [auth B],
SA [auth G],
T [auth B],
WA [auth H],
X [auth C],
XA [auth H],
Y [auth C],
YA [auth H],
ZA [auth H]
DIUNDECYL PHOSPHATIDYL CHOLINE
C32 H65 N O8 P
IJFVSSZAOYLHEE-SSEXGKCCSA-O
LMT
Query on LMT

Download Ideal Coordinates CCD File 
AB [auth H]
BB [auth H]
EA [auth D]
JA [auth E]
KB [auth J]
AB [auth H],
BB [auth H],
EA [auth D],
JA [auth E],
KB [auth J],
O [auth A],
OA [auth F],
TA [auth G],
U [auth B],
UA [auth G],
V [auth B],
Z [auth C]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
AA [auth C]
CB [auth H]
FA [auth D]
GB [auth I]
KA [auth E]
AA [auth C],
CB [auth H],
FA [auth D],
GB [auth I],
KA [auth E],
LB [auth J],
Q [auth A],
QA [auth F],
VA [auth G],
W [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
P [auth A],
PA [auth F]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.218 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 182.13α = 90
b = 133.49β = 102.64
c = 319.69γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
MOLREPphasing
BUSTERrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-05-16
    Type: Initial release
  • Version 1.1: 2012-05-30
    Changes: Database references
  • Version 1.2: 2012-06-27
    Changes: Database references
  • Version 1.3: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description