6VM3: Glycine receptor subunit alphaZ1

Full length Glycine receptor reconstituted in lipid nanodisc in Gly/IVM-conformation (State-3). Determined by electron microscopy at 3.07 Å resolution. Released 29 Jul 2020.

Method: Electron microscopy
Resolution: 3.07 Å
Organism: Danio rerio
Chains: 5
Atoms: 15,180
Mol. weight: 260.98 kDa
Ligands: IVM, GLY
Released: 29 Jul 2020

Explore 6VM3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6VM3 contains 50 α-helices and 70 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: 10 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	34-41	8
α-helix	53	1
α-helix	60	1
β-strand	61-76	16	1
β-strand	81-93	13	1
β-strand	108-109	2	1
α-helix	119-121	3
β-strand	123-124	2	2
β-strand	128-132	5	1
β-strand	140-144	5	1
β-strand	149-161	13	1
β-strand	173-181	9	2
β-strand	190-194	5	1
β-strand	200-202	3	1
β-strand	211-220	10	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	253-264	12
α-helix	273-294	22
α-helix	306-339	34
α-helix	396-443	48

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glycine receptor subunit alphaZ1	A, B, C, D, E	protein	444	Danio rerio	O93430 (AlphaFold model)

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

>6VM3_1 Glycine receptor subunit alphaZ1 (chains A, B, C, D, E)
MFALGIYLWETIVFFSLAASQQAAARKAASPMPPSEFLDKLMGKVSGYDARIRPNFKGPP
VNVTCNIFINSFGSIAETTMDYRVNIFLRQQWNDPRLAYSEYPDDSLDLDPSMLDSIWKP
DLFFANEKGANFHEVTTDNKLLRISKNGNVLYSIRITLVLACPMDLKNFPMDVQTCIMQL
ESFGYTMNDLIFEWDEKGAVQVADGLTLPQFILKEEKDLRYCTKHYNTGKFTCIEARFHL
ERQMGYYLIQMYIPSLLIVILSWVSFWINMDAAPARVGLGITTVLTMTTQSSGSRASLPK
VSYVKAIDIWMAVCLLFVFSALLEYAAVNFIARQHKELLRFQRRRRHLKEDEAGDGRFSF
AAYGMGPACLQAKDGMAIKGNNNNAPTSTNPPEKTVEEMRKLFISRAKRIDTVSRVAFPL
VFLIFNIFYWITYKIIRSEDIHKQ

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
GLY	Glycine	C2 H5 N O2	5

Primary citation

Mechanisms of activation and desensitization of full-length glycine receptor in lipid nanodiscs. Kumar, A., Basak, S., Rao, S. et al. Nat Commun (2020) 11:3752-3752. DOI 10.1038/s41467-020-17364-5 · 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…

Browse structure collections

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