8VUW | pdb_00008vuw

ELIC5 with cysteamine in 2:1:1 POPC:POPE:POPG nanodisc in open conformation

PDB DOI: https://doi.org/10.2210/pdb8VUW/pdb
Entry: 8VUW supersedes: 8D68
EM Map EMD-43542: EMDB EMDataResource

Classification: TRANSPORT PROTEIN
Organism(s): Dickeya chrysanthemi
Expression System: Escherichia coli
Mutation(s): Yes
Membrane Protein: Yes PDBTM MemProtMD mpstruc

Deposited: 2024-01-29 Released: 2024-02-07
Deposition Author(s): Petroff II, J.T., Deng, Z., Rau, M.J., Fitzpatrick, J.A.J., Yuan, P., Cheng, W.W.L.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.19 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

Open-channel structure of a pentameric ligand-gated ion channel reveals a mechanism of leaflet-specific phospholipid modulation.

Petroff, J.T., Dietzen, N.M., Santiago-McRae, E., Deng, B., Washington, M.S., Chen, L.J., Trent Moreland, K., Deng, Z., Rau, M., Fitzpatrick, J.A.J., Yuan, P., Joseph, T.T., Henin, J., Brannigan, G., Cheng, W.W.L.

(2022) Nat Commun 13: 7017

PubMed: 36385237 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-022-34813-5
Primary Citation Related Structures:
8D63, 8D64, 8D65, 8D66, 8D67, 8VUW

PubMed Abstract:
Pentameric ligand-gated ion channels (pLGICs) mediate synaptic transmission and are sensitive to their lipid environment. The mechanism of phospholipid modulation of any pLGIC is not well understood. We demonstrate that the model pLGIC, ELIC (Erwinia ligand-gated ion channel), is positively modulated by the anionic phospholipid, phosphatidylglycerol, from the outer leaflet of the membrane. To explore the mechanism of phosphatidylglycerol modulation, we determine a structure of ELIC in an open-channel conformation. The structure shows a bound phospholipid in an outer leaflet site, and structural changes in the phospholipid binding site unique to the open-channel. In combination with streamlined alchemical free energy perturbation calculations and functional measurements in asymmetric liposomes, the data support a mechanism by which an anionic phospholipid stabilizes the activated, open-channel state of a pLGIC by specific, state-dependent binding to this site.

Organizational Affiliation

Department of Anesthesiology, Washington University School of Medicine, Saint Louis, MO, USA.

Macromolecule Content

Total Structure Weight: 189.19 kDa
Atom Count: 13,055
Modeled Residue Count: 1,555
Deposited Residue Count: 1,610
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Erwinia chrysanthemi ligand-gated ion channel	A, B, C, D, E	322	Dickeya chrysanthemi	Mutation(s): 5 Membrane Entity: Yes
UniProt
Find proteins for P0C7B7 (Dickeya chrysanthemi) Explore P0C7B7 Go to UniProtKB: P0C7B7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0C7B7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGW (Subject of Investigation/LOI) Query on PGW Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth A] SDF format, chain I [auth B] SDF format, chain K [auth C] SDF format, chain M [auth D] MOL2 format, chain F [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth B] MOL2 format, chain K [auth C] MOL2 format, chain M [auth D] mmCIF format, chain F [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth B] mmCIF format, chain K [auth C] mmCIF format, chain M [auth D]	F [auth A], H [auth A], I [auth B], K [auth C], M [auth D]	(1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate C₄₀ H₇₇ O₁₀ P PAZGBAOHGQRCBP-HGWHEPCSSA-N		Interactions Focus chain F [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D]
DHL (Subject of Investigation/LOI) Query on DHL Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain L [auth C] SDF format, chain N [auth D] SDF format, chain O [auth E] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain L [auth C] MOL2 format, chain N [auth D] MOL2 format, chain O [auth E] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain L [auth C] mmCIF format, chain N [auth D] mmCIF format, chain O [auth E]	G [auth A], J [auth B], L [auth C], N [auth D], O [auth E]	2-AMINO-ETHANETHIOL C₂ H₇ N S UFULAYFCSOUIOV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain N [auth D] Focus chain O [auth E] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain N [auth D] Focus chain O [auth E]