8JJ3

Cryo-EM structure of nanodisc (PE:PS:PC) reconstituted GLIC at pH 2.5


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.65 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Cryo-EM structures of prokaryotic ligand-gated ion channel GLIC provide insights into gating in a lipid environment.

Bharambe, N.Li, Z.Seiferth, D.Balakrishna, A.M.Biggin, P.C.Basak, S.

(2024) Nat Commun 15: 2967-2967

  • DOI: https://doi.org/10.1038/s41467-024-47370-w
  • Primary Citation of Related Structures:  
    8I41, 8I42, 8I47, 8I48, 8JJ3, 8WCQ, 8WCR

  • PubMed Abstract: 

    GLIC, a proton-activated prokaryotic ligand-gated ion channel, served as a model system for understanding the eukaryotic counterparts due to their structural and functional similarities. Despite extensive studies conducted on GLIC, the molecular mechanism of channel gating in the lipid environment requires further investigation. Here, we present the cryo-EM structures of nanodisc-reconstituted GLIC at neutral and acidic pH in the resolution range of 2.6 - 3.4 Å. In our apo state at pH 7.5, the extracellular domain (ECD) displays conformational variations compared to the existing apo structures. At pH 4.0, three distinct conformational states (C1, C2 and O states) are identified. The protonated structures exhibit a compacted and counter-clockwise rotated ECD compared with our apo state. A gradual widening of the pore in the TMD is observed upon reducing the pH, with the widest pore in O state, accompanied by several layers of water pentagons. The pore radius and molecular dynamics (MD) simulations suggest that the O state represents an open conductive state. We also observe state-dependent interactions between several lipids and proteins that may be involved in the regulation of channel gating. Our results provide comprehensive insights into the importance of lipids impact on gating.


  • Organizational Affiliation

    School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Proton-gated ion channelA,
B [auth C],
C [auth B],
D,
E
312Gloeobacter violaceusMutation(s): 0 
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 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PEE (Subject of Investigation/LOI)
Query on PEE

Download Ideal Coordinates CCD File 
AB [auth E]
BA [auth B]
BB [auth E]
CA [auth B]
CB [auth E]
AB [auth E],
BA [auth B],
BB [auth E],
CA [auth B],
CB [auth E],
DA [auth B],
EA [auth B],
FA [auth B],
G [auth A],
GA [auth B],
H [auth A],
HA [auth B],
I [auth A],
IA [auth B],
J [auth A],
JA [auth D],
K [auth A],
L [auth A],
LA [auth D],
M [auth A],
MA [auth D],
N [auth A],
NA [auth D],
O [auth A],
OA [auth D],
PA [auth D],
Q [auth C],
QA [auth D],
R [auth C],
RA [auth D],
S [auth C],
SA [auth D],
T [auth C],
TA [auth E],
U [auth C],
V [auth C],
VA [auth E],
W [auth C],
WA [auth E],
X [auth C],
XA [auth E],
Y [auth C],
YA [auth E],
Z [auth B],
ZA [auth E]
1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
C41 H78 N O8 P
MWRBNPKJOOWZPW-NYVOMTAGSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
AA [auth B],
F [auth A],
KA [auth D],
P [auth C],
UA [auth E]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.65 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1
RECONSTRUCTIONRELION4.0.1

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateSingapore--

Revision History  (Full details and data files)

  • Version 1.0: 2024-04-17
    Type: Initial release