9LBD: Proton-gated ion channel

Cryo-EM structure of nanodisc (PE:PS:PC) reconstituted GLIC F116A mutant at pH 2.5. Determined by electron microscopy at 2.14 Å resolution. Released 22 Oct 2025.

Method: Electron microscopy
Resolution: 2.14 Å
Organism: Gloeobacter violaceus
Chains: 5
Atoms: 13,370
Mol. weight: 196.89 kDa
Ligands: PEE
Released: 22 Oct 2025

Explore 9LBD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9LBD contains 65 α-helices and 65 β-strands across 5 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chains A, B, C, D and E: 13 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	7-10	4
α-helix	14-15	2
β-strand	16-31	16	1
β-strand	36-48	13	1
α-helix	50-52	3
α-helix	56-59	4
β-strand	64-65	2	1
β-strand	76-78	3	2
β-strand	81	1	1
β-strand	86-94	9	1
β-strand	99-111	13	1
α-helix	119-121	3
β-strand	123-133	11	2
β-strand	140-144	5	1
α-helix	146-148	3
β-strand	150-151	2	1
β-strand	160-167	8	2
β-strand	172-175	4	2
β-strand	180-192	13	2
α-helix	197	1
α-helix	198-202	5
α-helix	203-212	10
α-helix	213-217	5
α-helix	221-242	22
α-helix	254-281	28
α-helix	285-315	31

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Proton-gated ion channel	A, B, C, D, E	protein	312	Gloeobacter violaceus	Q7NDN8 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E), FASTA

>9LBD_1 Proton-gated ion channel (chains A, B, C, D, E)
VSPPPPIADEPLTVNTGIYLIECYSLDDKAETFKVNAFLSLSWKDRRLAFDPVRSGVRVK
TYEPEAIWIPEIRFVNVENARDADVVDISVSPDGTVQYLERFSARVLSPLDARRYPFDSQ
TLHIYLIVRSVDTRNIVLAVDLEKVGKNDDVFLTGWDIESFTAVVKPANFALEDRLESKL
DYQLRISRQYFSYIPNIILPMLFILFISWTAFWSTSYEANVTLVVSTLIAHIAFNILVET
NLPKTPYMTYTGAIIFMIYLFYFVAVIEVTVQHYLKVESQPARAASITRASRIAFPVVFL
LANIILAFLFFG

Ligands and cofactors

ID	Name	Formula	Copies
PEE	1,2-dioleoyl-sn-glycero-3-phosphoethanolamine	C41 H78 N O8 P	25

Water and common crystallization additives (CL) are not listed.

Primary citation

Asymmetric gating of a homopentameric ion channel GLIC revealed by cryo-EM. Li, Z., Bharambe, N., Manishrao Lande, K. et al. Proc Natl Acad Sci U S A (2025) 122:e2512811122-e2512811122. DOI 10.1073/pnas.2512811122 · PubMed

Other PDB entries of the same protein (UniProt Q7NDN8 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6HZW 2.22 Å, THE GLIC PENTAMERIC LIGAND-GATED ION CHANNEL 2.22 resolution
3IGQ 2.3 Å, Crystal structure of the extracellular domain of a bacterial pentameric ligand-gated ion…
6F0U 2.35 Å, GLIC mutant E35A
4HFI 2.4 Å, The GLIC pentameric Ligand-Gated Ion Channel at 2.4 A resolution
6F0R 2.5 Å, GLIC mutant E82Q
6F0Z 2.5 Å, GLIC mutant D88N
6HJZ 2.5 Å, Xray structure of GLIC in complex with succinate
6HZ1 2.5 Å, The glic pentameric ligand-gated ion channel mutant E243C
6HY5 2.58 Å, The glic pentameric ligand-gated ion channel mutant Q193C
3TLW 2.6 Å, The GLIC pentameric Ligand-Gated Ion Channel Loop2-21' oxidized mutant in a…
5IUX 2.6 Å, GLIC-V135C bimane labelled X-ray structure
6F16 2.6 Å, GLIC mutant H277Q

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