8FE1: Glycine receptor subunit alphaZ1

Alpha1/BetaB Heteromeric Glycine Receptor in 1 mM Glycine 20 uM Ivermectin State. Determined by electron microscopy at 3.0 Å resolution. Released 22 Mar 2023.

Method: Electron microscopy
Resolution: 3.0 Å
Organism: Danio rerio
Chains: 5
Atoms: 15,445
Mol. weight: 294.8 kDa
Ligands: IVM, D10, PLM, PX4
Released: 22 Mar 2023

Explore 8FE1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8FE1 contains 58 α-helices and 77 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.

Chain A: 11 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	34-41	8
α-helix	60	1
β-strand	61-76	16	1
β-strand	81-93	13	1
β-strand	107-108	2	1
α-helix	109-110	2
α-helix	111-115	5
β-strand	122-124	3	2
β-strand	127-131	5	1
β-strand	140-144	5	1
β-strand	149-161	13	1
β-strand	173-182	10	2
β-strand	190-194	5	1
β-strand	200-202	3	1
β-strand	211-221	11	2
β-strand	224-225	2	3
β-strand	230-231	2	3
β-strand	233-242	10	2
α-helix	245-247	3
α-helix	248-252	5
α-helix	253-263	11
α-helix	264-266	3
α-helix	273-294	22
α-helix	306-333	28
α-helix	396-443	48

Chain B: 12 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	34-40	7
α-helix	53	1
α-helix	60	1
β-strand	61-76	16	11
β-strand	81-93	13	11
β-strand	106-109	4	11
α-helix	111-116	6
β-strand	122-124	3	12
β-strand	127-132	6	11
β-strand	140-145	6	11
β-strand	149-161	13	11
β-strand	173-182	10	12
β-strand	190-194	5	11
β-strand	200-202	3	11
β-strand	211-213	3	12
β-strand	218-221	4	12
β-strand	224-226	3	13
β-strand	229-231	3	13
β-strand	233-242	10	12
α-helix	245-247	3
α-helix	248-252	5
α-helix	253-263	11
α-helix	264-267	4
α-helix	273-294	22
α-helix	295-297	3
α-helix	306-337	32
α-helix	399-442	44

Chain C: 11 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	34-40	7
α-helix	53	1
α-helix	60	1
β-strand	61-76	16	8
β-strand	81-93	13	8
β-strand	106-109	4	8
α-helix	111-116	6
β-strand	123-124	2	9
β-strand	127-131	5	8
β-strand	140-145	6	8
β-strand	149-161	13	8
β-strand	173-181	9	9
β-strand	190-194	5	8
β-strand	200-202	3	8
β-strand	211-213	3	9
β-strand	218-221	4	9
β-strand	224-225	2	10
β-strand	230-231	2	10
β-strand	233-242	10	9
α-helix	245-247	3
α-helix	248-252	5
α-helix	253-263	11
α-helix	264-266	3
α-helix	273-296	24
α-helix	306-333	28
α-helix	397-443	47

Chain D: 13 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	34-40	7
α-helix	53	1
α-helix	60	1
β-strand	61-76	16	4
β-strand	81-93	13	4
α-helix	95-97	3
β-strand	107-108	2	4
α-helix	111-116	6
β-strand	122-124	3	5
β-strand	127-131	5	4
β-strand	134	1	6
β-strand	138	1	6
β-strand	140-144	5	4
β-strand	149-161	13	4
β-strand	173-182	10	5
β-strand	190-194	5	4
β-strand	200-202	3	4
β-strand	211-213	3	5
β-strand	218-221	4	5
β-strand	224-225	2	7
β-strand	230-231	2	7
β-strand	233-242	10	5
α-helix	243	1
α-helix	245-247	3
α-helix	248-252	5
α-helix	253-263	11
α-helix	264-267	4
α-helix	273-294	22
α-helix	306-333	28
α-helix	397-443	47

Chain E: 11 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	59-63	5
α-helix	79	1
β-strand	80-95	16	14
β-strand	100-112	13	14
α-helix	131-136	6
β-strand	142-144	3	15
β-strand	147-151	5	14
β-strand	154	1	16
β-strand	158	1	16
β-strand	160-164	5	14
β-strand	169-181	13	14
α-helix	189-191	3
β-strand	193-202	10	15
β-strand	210-214	5	14
β-strand	220-221	2	14
β-strand	230-232	3	15
β-strand	237	1	15
β-strand	244-246	3	17
β-strand	250-252	3	17
β-strand	254-263	10	15
α-helix	266-268	3
α-helix	269-273	5
α-helix	274-284	11
α-helix	285-287	3
α-helix	294-318	25
α-helix	327-354	28
α-helix	468-492	25

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glycine receptor subunit alphaZ1	A, B, C, D	protein	458	Danio rerio	O93430 (AlphaFold model)
Glycine receptor beta subunit 2	E	protein	591	Danio rerio	Q6DC22 (AlphaFold model)

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

>8FE1_1 Glycine receptor subunit alphaZ1 (chains A, B, C, D)
MFALGIYLWETIVFFSLAASQQAAARKAASPMPPSEFLDKLMGKVSGYDARIRPNFKGPP
VNVTCNIFINSFGSIAETTMDYRVNIFLRQQWNDPRLAYSEYPDDSLDLDPSMLDSIWKP
DLFFANEKGANFHEVTTDNKLLRISKNGNVLYSIRITLVLACPMDLKNFPMDVQTCIMQL
ESFGYTMNDLIFEWDEKGAVQVADGLTLPQFILKEEKDLRYCTKHYNTGKFTCIEARFHL
ERQMGYYLIQMYIPSLLIVILSWVSFWINMDAAPARVGLGITTVLTMTTQSSGSRASLPK
VSYVKAIDIWMAVCLLFVFSALLEYAAVNFIARQHKELLRFQRRRRHLKEDEAGDGRFSF
AAYGMGPACLQAKDGMAIKGNNNNAPTSTNPPEKTVEEMRKLFISRAKRIDTVSRVAFPL
VFLIFNIFYWITYKIIRSEDIHKQLVPRGSHHHHHHHH

Sequence of entity 2 (E), FASTA

>8FE1_2 Glycine receptor beta subunit 2 (chains E)
MKALKVIFMLLIICLWMEGGFTKEKSAKKWSHPQFEKGGGSGGGSGGGSWSHPQFEKGGG
SGGGSGGGSWSHPQFEKGGGSGGGSGGGSWSHPQFEKENLYFQGEKSAKKGKKKGKQVYC
PSQLSSEDLARVPANSTSNILNKLLITYDPRIRPNFKGIPVEDRVNIFINSFGSIQETTM
DYRVNIFLRQRWNDPRLRLPQDFKSDSLTVDPKMFKCLWKPDLFFANEKSANFHDVTQEN
ILLFIFRNGDVLISMRLSVTLSCPLDLTLFPMDTQRCKMQLESFGYTTDDLQFMWQSGDP
VQMDEIALPQFDIKQEDIEYGNCTKYYAGTGYYTCVEVIFTLRRQVGFYMMGVYAPTLLI
VVLSWLSFWINPDASAARVPLGILSVLSLSSECTSLASELPKVSYVKAIDIWLIACLLFG
FASLVEYAVVQVMLNSPKLLEAERAKIATKEKAEGKTPAKNTINGMGSTPIHVSTLQVTE
TRCKKVCTSKSDLRTNDFSIVGSLPRDFELSNFDCYGKPIEVGSAFSKSQAKNNKKPPPP
KPVIPSAAKRIDLYARALFPFSFLFFNVIYWSVYLENLYFQGTETSQVAPA

Ligands and cofactors

ID	Name	Formula	Copies
IVM	(2aE,4E,5'S,6S,6'R,7S,8E,11R,13R,15S,17aR,20R,20aR,20bS)-6'-[(2S)-butan-2-yl]-2…	C48 H74 O14	5
D10	Decane	C10 H22	1
PLM	Palmitic acid	C16 H32 O2	28
PX4	1,2-dimyristoyl-sn-glycero-3-phosphocholine	C36 H73 N O8 P	8
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	6
GLY	Glycine	C2 H5 N O2	5

Primary citation

Conformational transitions and allosteric modulation in a heteromeric glycine receptor. Gibbs, E., Klemm, E., Seiferth, D. et al. Nat Commun (2023) 14:1363-1363. DOI 10.1038/s41467-023-37106-7 · PubMed

Other PDB entries of the same protein (UniProt O93430 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7M6N 2.61 Å, Full length alpha1 Glycine receptor in presence of 0.1mM Glycine
7U2N 2.8 Å, A novel compound mimics the structural and functional effects of the full agonist…
7M6O 2.84 Å, Full length alpha1 Glycine receptor in presence of 0.1mM Glycine and 32uM…
6PLX 2.9 Å, CryoEM structure of zebra fish alpha-1 glycine receptor bound with GABA in SMA,…
6PLY 2.9 Å, CryoEM structure of zebra fish alpha-1 glycine receptor bound with GABA in SMA, open state
6PM6 2.9 Å, CryoEM structure of zebra fish alpha-1 glycine receptor bound with Glycine in SMA, open…
6PXD 2.9 Å, CryoEM structure of zebra fish alpha-1 glycine receptor, Apo state
7U2M 2.9 Å, A novel compound mimics the structural and functional effects of the full agonist…
7M6Q 2.91 Å, Full length alpha1 Glycine receptor in presence of 1mM Glycine and 32uM…
6PLS 3.0 Å, CryoEM structure of zebra fish alpha-1 glycine receptor bound with taurine in nanodisc,…
6PLW 3.0 Å, CryoEM structure of zebra fish alpha-1 glycine receptor bound with GABA in SMA,…
6PLZ 3.0 Å, CryoEM structure of zebra fish alpha-1 glycine receptor bound with GABA in SMA, closed…

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