6PM6: Zebra fish alpha-1 glycine receptor

CryoEM structure of zebra fish alpha-1 glycine receptor bound with Glycine in SMA, open state. Determined by electron microscopy at 2.9 Å resolution. Released 10 Feb 2021.

Method: Electron microscopy
Resolution: 2.9 Å
Organism: Danio rerio
Chains: 5
Atoms: 14,100
Mol. weight: 266 kDa
Ligands: GLY
Released: 10 Feb 2021

Explore 6PM6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6PM6 contains 76 α-helices and 75 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: 15 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	26-34	9
α-helix	37-39	3
α-helix	52	1
β-strand	53-68	16	1
β-strand	73-85	13	1
α-helix	87-89	3
β-strand	98-100	3	1
α-helix	105-107	3
β-strand	114-116	3	2
β-strand	122-123	2	1
β-strand	132-137	6	1
β-strand	141-153	13	1
α-helix	161-163	3
β-strand	165-174	10	2
β-strand	182-186	5	1
β-strand	192-194	3	1
β-strand	203-205	3	2
β-strand	211-213	3	2
β-strand	216-217	2	3
β-strand	222-223	2	3
β-strand	225-234	10	2
α-helix	239	1
α-helix	240-244	5
α-helix	245-247	3
α-helix	249-256	8
α-helix	267-285	19
α-helix	300-303	4
α-helix	305-324	20
α-helix	394-405	12
α-helix	410-426	17

Chain B: 16 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	26-34	9
α-helix	37-39	3
α-helix	52	1
β-strand	53-68	16	7
β-strand	73-85	13	7
α-helix	87-89	3
β-strand	98-100	3	7
α-helix	105-107	3
β-strand	114-116	3	8
β-strand	122-124	3	7
β-strand	132-137	6	7
β-strand	141-153	13	7
α-helix	161-163	3
β-strand	165-174	10	8
β-strand	182-186	5	7
β-strand	192-194	3	7
β-strand	203-205	3	8
β-strand	211-213	3	8
β-strand	216-217	2	9
β-strand	222-223	2	9
β-strand	225-234	10	8
α-helix	236-238	3
α-helix	239	1
α-helix	240-244	5
α-helix	245-247	3
α-helix	249-256	8
α-helix	267-285	19
α-helix	300-303	4
α-helix	305-324	20
α-helix	392-405	14
α-helix	410-426	17

Chain C: 15 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	26-34	9
α-helix	37-39	3
α-helix	52	1
β-strand	53-68	16	10
β-strand	73-85	13	10
α-helix	87-89	3
β-strand	98-100	3	10
α-helix	105-107	3
β-strand	114-116	3	11
β-strand	122-124	3	10
β-strand	132-137	6	10
β-strand	141-153	13	10
α-helix	161-163	3
β-strand	165-174	10	11
β-strand	182-186	5	10
β-strand	192-194	3	10
β-strand	203-205	3	11
β-strand	211-213	3	11
β-strand	216-217	2	12
β-strand	222-223	2	12
β-strand	225-234	10	11
α-helix	239	1
α-helix	240-244	5
α-helix	245-247	3
α-helix	249-256	8
α-helix	267-285	19
α-helix	300-303	4
α-helix	305-324	20
α-helix	392-405	14
α-helix	410-426	17

Chain D: 15 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	26-34	9
α-helix	37-39	3
α-helix	52	1
β-strand	53-68	16	4
β-strand	73-85	13	4
α-helix	87-89	3
β-strand	98-100	3	4
α-helix	105-107	3
β-strand	114-116	3	5
β-strand	122-124	3	4
β-strand	132-137	6	4
β-strand	141-153	13	4
α-helix	161-163	3
β-strand	165-174	10	5
β-strand	182-186	5	4
β-strand	192-194	3	4
β-strand	203-205	3	5
β-strand	211-213	3	5
β-strand	216-217	2	6
β-strand	222-223	2	6
β-strand	225-234	10	5
α-helix	237-239	3
α-helix	240-244	5
α-helix	245-247	3
α-helix	249-256	8
α-helix	267-285	19
α-helix	300-303	4
α-helix	305-324	20
α-helix	391-405	15
α-helix	410-426	17

Chain E: 15 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	26-34	9
α-helix	37-39	3
α-helix	52	1
β-strand	53-68	16	13
β-strand	73-85	13	13
α-helix	87-89	3
β-strand	98-100	3	13
α-helix	105-107	3
β-strand	114-116	3	14
β-strand	122-124	3	13
β-strand	132-137	6	13
β-strand	141-153	13	13
α-helix	161-163	3
β-strand	165-174	10	14
β-strand	182-186	5	13
β-strand	192-194	3	13
β-strand	203-205	3	14
β-strand	211-213	3	14
β-strand	216-217	2	15
β-strand	222-223	2	15
β-strand	225-234	10	14
α-helix	239	1
α-helix	240-244	5
α-helix	245-247	3
α-helix	249-256	8
α-helix	266-285	20
α-helix	300-303	4
α-helix	305-324	20
α-helix	392-405	14
α-helix	410-426	17

Molecules and chains

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

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

>6PM6_1 Glycine receptor subunit alphaZ1 (chains A, B, C, D, E)
MFALGIYLWETIVFFSLAASQQAAARKAASPMPPSEFLDKLMGKVSGYDARIRPNFKGPP
VNVTCNIFINSFGSIAETTMDYRVNIFLRQQWNDPRLAYSEYPDDSLDLDPSMLDSIWKP
DLFFANEKGANFHEVTTDNKLLRISKNGNVLYSIRITLVLACPMDLKNFPMDVQTCIMQL
ESFGYTMNDLIFEWDEKGAVQVADGLTLPQFILKEEKDLRYCTKHYNTGKFTCIEARFHL
ERQMGYYLIQMYIPSLLIVILSWVSFWINMDAAPARVGLGITTVLTMTTQSSGSRASLPK
VSYVKAIDIWMAVCLLFVFSALLEYAAVNFIARQHKELLRFQRRRRHLKEDEAGDGRFSF
AAYGMGPACLQAKDGMAIKGNNNNAPTSTNPPEKTVEEMRKLFISRAKRIDTVSRVAFPL
VFLIFNIFYWITYKIIRSEDIHKQLVPRGSHHHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
GLY	Glycine	C2 H5 N O2	5

Primary citation

Mechanism of gating and partial agonist action in the glycine receptor. Yu, J., Zhu, H., Lape, R. et al. Cell (2021) 184:957-968.e21. DOI 10.1016/j.cell.2021.01.026 · 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
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…
6PM1 3.0 Å, CryoEM structure of zebra fish alpha-1 glycine receptor bound with Taurine in SMA,…

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