7EPB: LY354740-bound mGlu2 homodimer

Cryo-EM structure of LY354740-bound mGlu2 homodimer. Determined by electron microscopy at 3.1 Å resolution. Released 23 Jun 2021.

Method: Electron microscopy
Resolution: 3.1 Å
Organisms: Homo sapiens, Lama glama
Chains: 4
Atoms: 13,104
Mol. weight: 218.91 kDa
Ligands: 40F
Released: 23 Jun 2021

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

Secondary structure: helices and β-sheets

7EPB contains 57 α-helices and 70 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: 28 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	26-28	3	1
β-strand	32-38	7	1
β-strand	41	1	2
β-strand	53	1	2
α-helix	54	1
α-helix	55-60	6
α-helix	61-73	13
β-strand	84-90	7	1
α-helix	95-114	20
α-helix	133-135	3
β-strand	138-141	4	1
α-helix	145-156	12
β-strand	162-163	2	1
α-helix	170-172	3
α-helix	188-201	14
β-strand	206-210	5	3
α-helix	216-230	15
β-strand	234-239	6	3
α-helix	247-257	11
β-strand	265-268	4	3
α-helix	272-284	13
β-strand	290-293	4	3
β-strand	315-319	5	3
α-helix	325-332	8
α-helix	345-353	9
α-helix	378-399	22
α-helix	408-410	3
α-helix	415-418	4
α-helix	419-423	5
β-strand	427-429	3	4
α-helix	430	1
β-strand	440-442	3	4
β-strand	453-459	7	3
β-strand	467-474	8	3
β-strand	478-480	3	3
α-helix	490-492	3
β-strand	510-511	2	5
β-strand	522-523	2	5
β-strand	530	1	6
β-strand	538	1	6
β-strand	545	1	7
β-strand	554	1	7
α-helix	557-559	3
α-helix	569-591	23
α-helix	598-600	3
α-helix	603-624	22
α-helix	632-658	27
α-helix	678-700	23
α-helix	725-746	22
α-helix	758-782	25
α-helix	787-815	29

Chain B: 29 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	26-28	3	8
β-strand	32-38	7	8
β-strand	41	1	9
β-strand	53	1	9
α-helix	54	1
α-helix	55-59	5
α-helix	60-73	14
β-strand	84-90	7	8
α-helix	95-114	20
α-helix	133-135	3
β-strand	138-141	4	8
α-helix	145-156	12
β-strand	162-163	2	8
α-helix	170-172	3
α-helix	188-201	14
β-strand	206-210	5	10
α-helix	215-229	15
β-strand	234-239	6	10
α-helix	247-257	11
β-strand	265-268	4	10
α-helix	272-284	13
β-strand	290-293	4	10
β-strand	315-319	5	10
α-helix	325-332	8
α-helix	345-353	9
α-helix	378-396	19
α-helix	408-410	3
α-helix	415-418	4
α-helix	419-423	5
β-strand	427-429	3	11
α-helix	430	1
β-strand	440-442	3	11
β-strand	453-459	7	10
β-strand	467-474	8	10
β-strand	478-480	3	10
α-helix	490-492	3
β-strand	509-511	3	12
β-strand	522-524	3	12
β-strand	530	1	13
β-strand	538	1	13
β-strand	545	1	14
β-strand	554	1	14
α-helix	569-591	23
α-helix	596-599	4
α-helix	603-625	23
α-helix	632-656	25
α-helix	678-700	23
α-helix	726-746	21
α-helix	747-749	3
α-helix	758-782	25
α-helix	783-785	3
α-helix	788-815	28

Chain C: 0 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	15
β-strand	18-24	7	15
β-strand	31-39	9	16
β-strand	46-51	6	16
β-strand	57	1	16
β-strand	69-72	4	15
β-strand	77-82	6	15
β-strand	92-99	8	16
β-strand	105-108	4	16
β-strand	109	1	15
β-strand	112	1	16

Chain D: 0 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	17
β-strand	10-12	3	18
β-strand	18-24	7	17
β-strand	31-39	9	19
β-strand	46-51	6	19
β-strand	57-59	3	19
β-strand	69-72	4	17
β-strand	77-82	6	17
β-strand	92-99	8	19
β-strand	106-107	2	19
β-strand	109	1	17
β-strand	112	1	19
β-strand	114-116	3	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Metabotropic glutamate receptor 2	A, B	protein	851	Homo sapiens	Q14416 (AlphaFold model)
Anti-RON nanobody	C, D	protein	137	Lama glama

Sequence of entity 1 (A, B), FASTA

>7EPB_1 Metabotropic glutamate receptor 2 (chains A, B)
DYKDDDDGAPEGPAKKVLTLEGDLVLGGLFPVHQKGGPAEDCGPVNEHRGIQRLEAMLFA
LDRINRDPHLLPGVRLGAHILDSCSKDTHALEQALDFVRASLSRGADGSRHICPDGSYAT
HGDAPTAITGVIGGSYSDVSIQVANLLRLFQIPQISYASTSAKLSDKSRYDYFARTVPPD
FFQAKAMAEILRFFNWTYVSTVASEGDYGETGIEAFELEARARNICVATSEKVGRAMSRA
AFEGVVRALLQKPSARVAVLFTRSEDARELLAASQRLNASFTWVASDGWGALESVVAGSE
GAAEGAITIELASYPISDFASYFQSLDPWNNSRNPWFREFWEQRFRCSFRQRDCAAHSLR
AVPFEQESKIMFVVNAVYAMAHALHNMHRALCPNTTRLCDAMRPVNGRRLYKDFVLNVKF
DAPFRPADTHNEVRFDRFGDGIGRYNIFTYLRAGSGRYRYQKVGYWAEGLTLDTSLIPWA
SPSAGPLPASRCSEPCLQNEVKSVQPGEVCCWLCIPCQPYEYRLDEFTCADCGLGYWPNA
SLTGCFELPQEYIRWGDAWAVGPVTIACLGALATLFVLGVFVRHNATPVVKAAGRELCYI
LLGGVFLCYCMTFIFIAKPSTAVCTLRRLGLGTAFSVCYSALLTKTNRIARIFGGAREGA
QRPRFISPASQVAICLALISGQLLIVVAWLVVEAPGTGKETAPERREVVTLRCNHRDASM
LGSLAYNVLLIALCTLYAFKTRKCPENFNEAKFIGFTMYTTCIIWLAFLPIFYVTSSDYR
VQTTTMCVSVSLSGSVVLGCLFAPKLHIILFQPQKNVEFLEVLFQGPGSGSWSHPQFEKG
SGSWSHPQFEK

Sequence of entity 2 (C, D), FASTA

>7EPB_2 Anti-RON nanobody (chains C, D)
QVQLVQSGGGLVQAGGSLRLSCAASVRFFSINTMGWYRQAPGKQRELVADITSSGSTNYA
DSGKGRFTISRDNAKNTVYLQMNRLKPEDTAVYYCHADYKYTTHNTAWGQGTQVTVSSGR
PLEVLFQGPHHHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
40F	(1S,2S,5R,6S)-2-aminobicyclo[3.1.0]hexane-2,6-dicarboxylic acid	C8 H11 N O4	2

Primary citation

Structures of human mGlu2 and mGlu7 homo- and heterodimers. Du, J., Wang, D., Fan, H. et al. Nature (2021) 594:589-593. DOI 10.1038/s41586-021-03641-w · PubMed

Other PDB entries of the same protein (UniProt Q14416 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4XAQ 2.21 Å, mGluR2 ECD and mGluR3 ECD with ligands
4XAS 2.35 Å, mGluR2 ECD ligand complex
7EPE 2.5 Å, Crystal structure of mGlu2 bound to NAM563
5CNJ 2.65 Å, mGlur2 with glutamate analog
5CNI 2.69 Å, mGlu2 with Glutamate
7EPF 2.7 Å, Crystal structure of mGlu2 bound to NAM597
5KZN 2.8 Å, Metabotropic Glutamate Receptor
5KZQ 2.8 Å, Metabotropic Glutamate Receptor in complex with antagonist…
8JCU 2.8 Å, Cryo-EM structure of mGlu2-mGlu3 heterodimer in presence of LY341495 (dimerization mode I)
8JD2 2.8 Å, Cryo-EM structure of G protein-free mGlu2-mGlu3 heterodimer in Acc state
8JCY 2.9 Å, Cryo-EM structure of mGlu2-mGlu3 heterodimer in presence of LY341495, NAM563, and…
8JD4 2.9 Å, Cryo-EM structure of G protein-free mGlu2-mGlu4 heterodimer in Acc state

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