7DGE: Intermediate state of class C GPCR

intermediate state of class C GPCR. Determined by electron microscopy at 3.65 Å resolution. Released 22 Sept 2021.

Method: Electron microscopy
Resolution: 3.65 Å
Organisms: Homo sapiens, Lama glama
Chains: 4
Atoms: 14,249
Mol. weight: 213.7 kDa
Ligands: QUS
Released: 22 Sept 2021

Explore 7DGE in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7DGE contains 70 α-helices and 81 β-strands across 4 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: 33 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	39-41	3	1
β-strand	45	1	2
β-strand	46-51	6	1
β-strand	54	1	3
α-helix	55-58	4
β-strand	70	1	3
α-helix	76-91	16
β-strand	101	1	2
β-strand	103-107	5	1
α-helix	112-127	16
β-strand	156-160	5	1
α-helix	165-175	11
α-helix	176-178	3
β-strand	182-184	3	1
α-helix	190-193	4
β-strand	201-203	3	1
α-helix	209-221	13
β-strand	226-232	7	4
α-helix	235-250	16
β-strand	254-261	8	4
α-helix	267-278	12
α-helix	293-306	14
α-helix	318-320	3
α-helix	332-334	3
β-strand	338-342	5	5
α-helix	345-347	3
α-helix	348-355	8
α-helix	368-375	8
α-helix	393-395	3
α-helix	410-431	22
α-helix	447-456	10
β-strand	459-460	2	6
β-strand	466-467	2	6
β-strand	479-486	8	5
β-strand	492-501	10	5
β-strand	504-507	4	5
β-strand	534-535	2	7
β-strand	547-548	2	7
β-strand	554-558	5	8
β-strand	561-564	4	8
α-helix	565-566	2
β-strand	569-571	3	9
α-helix	573-575	3
β-strand	578-580	3	9
β-strand	586	1	10
α-helix	591-611	21
α-helix	612-616	5
α-helix	628-648	21
β-strand	650	1	10
α-helix	654-661	8
α-helix	662-666	5
α-helix	667-686	20
α-helix	703-727	25
β-strand	732	1	11
α-helix	745	1
β-strand	746	1	11
α-helix	747	1
α-helix	751-774	24
α-helix	783-805	23
α-helix	812-830	19
α-helix	832-837	6

Chain B: 33 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	39-41	3	12
β-strand	45-51	7	12
β-strand	54	1	13
α-helix	55-58	4
β-strand	70	1	13
α-helix	76-89	14
β-strand	101-107	7	12
α-helix	112-127	16
β-strand	158-160	3	12
α-helix	165-176	12
β-strand	182-183	2	12
α-helix	190-193	4
β-strand	201-202	2	12
α-helix	208-221	14
β-strand	226	1	14
β-strand	228-232	5	15
α-helix	235-251	17
β-strand	254	1	14
β-strand	258-261	4	15
α-helix	267-280	14
β-strand	286-290	5	15
α-helix	293-306	14
β-strand	313-316	4	15
α-helix	318-320	3
α-helix	325-327	3
α-helix	331-333	3
β-strand	338-342	5	16
α-helix	348-355	8
α-helix	369-375	7
β-strand	379	1	17
β-strand	393	1	17
α-helix	410-431	22
α-helix	448-455	8
α-helix	465-467	3
β-strand	479-483	5	16
β-strand	486	1	18
β-strand	492	1	18
β-strand	495-500	6	16
β-strand	505-506	2	16
α-helix	509-511	3
α-helix	513-515	3
β-strand	533-535	3	19
β-strand	547-549	3	19
α-helix	550-551	2
α-helix	565-566	2
β-strand	569-570	2	20
α-helix	571-572	2
α-helix	573-575	3
β-strand	579-580	2	20
α-helix	581-582	2
α-helix	591-617	27
α-helix	628-643	16
α-helix	657-688	32
α-helix	705-726	22
β-strand	732	1	21
β-strand	746	1	21
α-helix	751-770	20
α-helix	771-773	3
α-helix	783-806	24
α-helix	812-830	19
α-helix	832-837	6

Chain C: 2 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	22
β-strand	14-15	2	23
β-strand	20-27	8	22
β-strand	35-41	7	24
β-strand	48-53	6	24
β-strand	60-62	3	24
α-helix	64-66	3
β-strand	71-75	5	22
β-strand	80-85	6	22
α-helix	90-92	3
β-strand	94	1	25
β-strand	95-101	7	24
β-strand	112-115	4	24
β-strand	121	1	25
β-strand	123-124	2	23

Chain D: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	6-9	4	26
β-strand	14	1	27
β-strand	20-26	7	26
α-helix	31-33	3
β-strand	35-41	7	28
β-strand	48-53	6	28
β-strand	60-62	3	28
α-helix	64-66	3
β-strand	70-75	6	26
β-strand	80-85	6	26
β-strand	95-101	7	28
β-strand	114-115	2	28
β-strand	120	1	28
β-strand	123	1	27

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Metabotropic glutamate receptor 1	A, B	protein	833	Homo sapiens	Q13255 (AlphaFold model)
nanobody	C, D	protein	123	Lama glama

Sequence of entity 1 (A, B), FASTA

>7DGE_1 Metabotropic glutamate receptor 1 (chains A, B)
GASSQRSVARMDGDVIIGALFSVHHQPPAEKVPERKCGEIREQYGIQRVEAMFHTLDKIN
ADPVLLPNITLGSEIRDSCWHSSVALEQSIEFIRDSLISIRDEKDGINRCLPDGQSLPPG
RTKKPIAGVIGPGSSSVAIQVQNLLQLFDIPQIAYSATSIDLSDKTLYKYFLRVVPSDTL
QARAMLDIVKRYNWTYVSAVHTEGNYGESGMDAFKELAAQEGLCIAHSDKIYSNAGEKSF
DRLLRKLRERLPKARVVVCFCEGMTVRGLLSAMRRLGVVGEFSLIGSDGWADRDEVIEGY
EVEANGGITIKLQSPEVRSFDDYFLKLRLDTNHRNPWFQEFWQHRFQCRLEGFPQENSNF
KRICTGNESLEENYVQDSKMGFVINAIYAMAHGLQNMHHALCPGHVGLCDAMKPIDGSKL
LDFLIKSSFIGVSGEEVWFDEKGDAPGRYDIMNLQYTEANRYDYVHVGTWHEGVLNIDDY
KIQMNKSGVVRSVCSEPCLKGQIKVIRKGEVSCCWICTACKENEYVQDEFTCKACDLGWW
PNADLTGCEPIPVRYLEWSNIESIIAIAFSCLGILVTLFVTLIFVLYRDTPVVKSSSREL
CYIILAGIFLGYVCPFTLIAKPTTTSCYLQRLLVGLSSAMCYSALVTKTNRIARILAGSK
KKICTRKPRFMSAWAQVIIASILISVQLTLVVTLIIMEPPMPILSYPSIKEVYLICNTSN
LGVVAPLGYNGLLIMSCTYYAFKTRNVPANFNEAKYIAFTMYTTCIIWLAFVPIYFGSNY
KIITTCFAVSLSVTVALGCMFTPKMYIIIAKPERNVRSAFTTSDVVRMHVGDG

Sequence of entity 2 (C, D), FASTA

>7DGE_2 nanobody (chains C, D)
QVQLVESGGGLVQAGGSLRLSCAASGRTFTSYAMGWFRQAPGKERESVAAISSSGGSTHY
ADSVKGRFTISRDNSKNTVYLQMNSLKPEDTAVYYCAAAMYGSRWPDWEYDYWGQGTQVT
VSS

Ligands and cofactors

ID	Name	Formula	Copies
QUS	(s)-2-amino-3-(3,5-dioxo-[1,2,4]OXADIAZOLIDIN-2-yl)-propionic acid	C5 H7 N3 O5	1

Primary citation

Structural insights into the activation initiation of full-length mGlu1. Zhang, J., Qu, L., Wu, L. et al. Protein Cell (2021) 12:662-667. DOI 10.1007/s13238-020-00808-5 · PubMed

Other PDB entries of the same protein (UniProt Q13255 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3KS9 1.9 Å, Metabotropic glutamate receptor mGluR1 complexed with LY341495 antagonist
4OR2 2.8 Å, Human class C G protein-coupled metabotropic glutamate receptor 1 in complex with a…
9WQO 2.9 Å, GRM1-Acc State Conformation 1
27TM 3.2 Å, GRM1-Acc State Conformation 2
9WQM 3.3 Å, GRM1-Gi Complex Structure
9WQN 3.7 Å, GRM1-Gq Complex Structure
7DGD 3.96 Å, apo state of class C GPCR

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