6HJZ: Xray structure of GLIC

Xray structure of GLIC in complex with succinate. Determined by X-ray diffraction at 2.5 Å resolution. Released 18 Sept 2019.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Gloeobacter violaceus (strain PCC 7421)
Chains: 10
Atoms: 26,501
Mol. weight: 390.72 kDa
Ligands: PLC, LMT, SIN
Released: 18 Sept 2019

Explore 6HJZ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6HJZ contains 130 α-helices and 120 β-strands across 10 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.

Chain A: 13 helices, 12 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
α-helix	68-70	3
β-strand	76-78	3	2
β-strand	81	1	1
β-strand	86-94	9	1
β-strand	99-111	13	1
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	160-176	17	2
β-strand	179-192	14	2
α-helix	197	1
α-helix	198-202	5
α-helix	203-212	10
α-helix	213-217	5
α-helix	221-244	24
α-helix	254-281	28
α-helix	285-314	30

Chains B, C, D, E, F and H: 13 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	7-10	4
α-helix	14-15	2
β-strand	16-31	16	3
β-strand	36-48	13	3
α-helix	50-52	3
α-helix	56-59	4
β-strand	64-65	2	3
α-helix	68-70	3
β-strand	76-78	3	4
β-strand	81	1	3
β-strand	86-94	9	3
β-strand	99-111	13	3
β-strand	123-133	11	4
β-strand	140-144	5	3
α-helix	146-148	3
β-strand	150-151	2	3
β-strand	160-176	17	4
β-strand	179-192	14	4
α-helix	197	1
α-helix	198-202	5
α-helix	203-212	10
α-helix	213-217	5
α-helix	221-245	25
α-helix	254-281	28
α-helix	285-314	30

Chain G: 14 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	7-10	4
α-helix	14-15	2
β-strand	16-31	16	13
β-strand	36-48	13	13
α-helix	50-52	3
α-helix	56-59	4
β-strand	64-65	2	13
α-helix	68-70	3
β-strand	76-78	3	14
β-strand	81	1	13
β-strand	86-94	9	13
β-strand	99-111	13	13
β-strand	123-133	11	14
β-strand	140-144	5	13
α-helix	146-148	3
β-strand	150-151	2	13
β-strand	160-176	17	14
β-strand	179-192	14	14
α-helix	197	1
α-helix	198-202	5
α-helix	203-212	10
α-helix	213-217	5
α-helix	221-244	24
α-helix	247-249	3
α-helix	254-281	28
α-helix	285-314	30

Chain I: 13 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	7-10	4
α-helix	14-15	2
β-strand	16-31	16	17
β-strand	36-48	13	17
α-helix	50-52	3
α-helix	56-59	4
β-strand	64-65	2	17
α-helix	68-70	3
β-strand	76-78	3	18
β-strand	81	1	17
β-strand	86-94	9	17
β-strand	99-111	13	17
β-strand	123-133	11	18
β-strand	140-144	5	17
α-helix	146-148	3
β-strand	150-151	2	17
β-strand	160-175	16	18
β-strand	180-192	13	18
α-helix	197	1
α-helix	198-202	5
α-helix	203-212	10
α-helix	213-217	5
α-helix	221-245	25
α-helix	254-281	28
α-helix	285-314	30

Chain J: 12 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	7-10	4
α-helix	14-15	2
β-strand	16-31	16	19
β-strand	36-48	13	19
α-helix	50-52	3
β-strand	64-65	2	19
α-helix	68-70	3
β-strand	76-78	3	20
β-strand	81	1	19
β-strand	86-94	9	19
β-strand	99-111	13	19
β-strand	123-133	11	20
β-strand	140-144	5	19
α-helix	146-148	3
β-strand	150-151	2	19
β-strand	160-176	17	20
β-strand	179-192	14	20
α-helix	197	1
α-helix	198-202	5
α-helix	203-212	10
α-helix	213-217	5
α-helix	221-245	25
α-helix	254-281	28
α-helix	285-314	30

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Proton-gated ion channel	A, B, C, D, E, F, G, H, I, J	protein	317	Gloeobacter violaceus (strain PCC 7421)	Q7NDN8 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F, G, H, I, J), FASTA

>6HJZ_1 Proton-gated ion channel (chains A, B, C, D, E, F, G, H, I, J)
GQDMVSPPPPIADEPLTVNTGIYLIECYSLDDKAETFKVNAFLSLSWKDRRLAFDPVRSG
VRVKTYEPEAIWIPEIRFVNVENARDADVVDISVSPDGTVQYLERFSARVLSPLDFRRYP
FDSQTLHIYLIVRSVDTRNIVLAVDLEKVGKNDDVFLTGWDIESFTAVVKPANFALEDRL
ESKLDYQLRISRQYFSYIPNIILPMLFILFISWTAFWSTSYEANVTLVVSTLIAHIAFNI
LVETNLPKTPYMTYTGAIIFMIYLFYFVAVIEVTVQHYLKVESQPARAASITRASRIAFP
VVFLLANIILAFLFFGF

Ligands and cofactors

ID	Name	Formula	Copies
PLC	Diundecyl phosphatidyl choline	C32 H65 N O8 P	30
LMT	Dodecyl-beta-D-maltoside	C24 H46 O11	12
SIN	Succinic acid	C4 H6 O4	20

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

Primary citation

Structural evidence for the binding of monocarboxylates and dicarboxylates at pharmacologically relevant extracellular sites of a pentameric ligand-gated ion channel. Fourati, Z., Sauguet, L., Delarue, M. Acta Crystallogr D Struct Biol (2020) 76:668-675. DOI 10.1107/S205979832000772X · PubMed

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

9LBD 2.14 Å, Cryo-EM structure of nanodisc (PE:PS:PC) reconstituted GLIC F116A mutant at pH 2.5
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
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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