9II2: 2:2 Complex of mGlu3 and beta-arrestin1

Cryo-EM Structure of the 2:2 Complex of mGlu3 and beta-arrestin1. Determined by electron microscopy at 3.7 Å resolution. Released 5 Mar 2025.

Method: Electron microscopy
Resolution: 3.7 Å
Organisms: Homo sapiens, Mus musculus
Chains: 6
Atoms: 21,112
Mol. weight: 350.17 kDa
Ligands: CLR, GLU
Released: 5 Mar 2025

Explore 9II2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9II2 contains 92 α-helices and 158 β-strands across 6 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 and C: 9 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	6-12	7	12
β-strand	18-22	5	12
β-strand	26	1	13
β-strand	29	1	14
β-strand	34	1	14
β-strand	37-43	7	12
β-strand	54-63	10	11
α-helix	66-71	6
β-strand	75-85	11	11
α-helix	99-108	10
β-strand	113-117	5	12
β-strand	127-129	3	11
α-helix	130-131	2
α-helix	139	1
β-strand	140-149	10	11
α-helix	157-158	2
β-strand	164-168	5	11
β-strand	169	1	13
α-helix	180-182	3
β-strand	183-189	7	15
β-strand	196-203	8	15
β-strand	207-208	2	16
β-strand	214-222	9	15
β-strand	231-241	11	17
α-helix	243-245	3
α-helix	246-248	3
β-strand	249-258	10	17
β-strand	266-274	9	15
β-strand	288-290	3	11
β-strand	300	1	11
α-helix	301-302	2
β-strand	317-328	12	17
β-strand	342-349	8	17
β-strand	350-351	2	16

Chain B: 35 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	33-34	2	23
β-strand	39-45	7	23
β-strand	48	1	24
β-strand	60	1	24
α-helix	62-66	5
α-helix	67-81	15
β-strand	91-97	7	23
α-helix	102-113	12
α-helix	116-120	5
α-helix	138-140	3
β-strand	142-147	6	23
α-helix	151-161	11
β-strand	168-170	3	23
α-helix	176-178	3
β-strand	187-189	3	23
α-helix	194-207	14
β-strand	212-218	7	25
α-helix	222-236	15
β-strand	240-247	8	25
α-helix	253-264	12
β-strand	271-275	5	25
α-helix	278-290	13
β-strand	296-298	3	25
α-helix	307-312	6
β-strand	321-325	5	26
α-helix	331-338	8
α-helix	351-359	9
β-strand	362	1	27
β-strand	372	1	27
α-helix	390-411	22
α-helix	420-423	4
α-helix	427-434	8
β-strand	439-441	3	28
β-strand	453-455	3	28
β-strand	466-470	5	26
β-strand	473	1	29
β-strand	478	1	29
β-strand	481-486	6	26
β-strand	490-492	3	26
α-helix	494-496	3
α-helix	500-502	3
α-helix	533-535	3
β-strand	538-539	2	30
β-strand	547-548	2	30
β-strand	553-555	3	31
β-strand	562-564	3	31
α-helix	565-566	2
β-strand	567-568	2	32
α-helix	578-600	23
α-helix	605-610	6
α-helix	612-632	21
α-helix	638-671	34
α-helix	674	1
α-helix	681-683	3
α-helix	684-688	5
α-helix	689-709	21
β-strand	714-717	4	32
β-strand	726-730	5	32
α-helix	734-757	24
α-helix	763-791	29
α-helix	792-794	3
α-helix	796-814	19
α-helix	815-819	5
α-helix	820-827	8
β-strand	836	1	33
β-strand	857-862	6	34

Chains D and S: 2 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	6-8	3	40
β-strand	11-13	3	41
β-strand	20-25	6	40
β-strand	34-39	6	41
β-strand	46-50	5	41
β-strand	54-55	2	41
α-helix	56	1
β-strand	63-68	6	40
β-strand	71-76	6	40
β-strand	86-91	6	41
β-strand	99	1	41
β-strand	103-106	4	41
β-strand	1007-1010	4	42
β-strand	1013-1014	2	43
β-strand	1018-1027	10	42
α-helix	1032-1034	3
β-strand	1035-1042	8	44
β-strand	1048-1055	8	44
β-strand	1060-1063	4	44
β-strand	1071-1076	6	42
β-strand	1081-1089	9	42
β-strand	1096-1103	8	44
β-strand	1112	1	44
β-strand	1117	1	44
β-strand	1119-1120	2	43

Chain R: 35 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	33-34	2	1
β-strand	39-45	7	1
β-strand	48	1	2
β-strand	60	1	2
α-helix	62-66	5
α-helix	67-81	15
β-strand	91-97	7	1
α-helix	102-113	12
α-helix	116-120	5
α-helix	138-140	3
β-strand	142-147	6	1
α-helix	151-161	11
β-strand	168-170	3	1
α-helix	176-178	3
β-strand	187-189	3	1
α-helix	194-207	14
β-strand	212-218	7	3
α-helix	222-236	15
β-strand	240-247	8	3
α-helix	253-264	12
β-strand	271-275	5	3
α-helix	278-290	13
β-strand	296-298	3	3
α-helix	307-312	6
β-strand	321-325	5	4
α-helix	331-338	8
α-helix	351-359	9
β-strand	362	1	5
β-strand	372	1	5
α-helix	390-411	22
α-helix	421-423	3
α-helix	427-434	8
β-strand	439-441	3	6
β-strand	453-455	3	6
β-strand	466-470	5	4
β-strand	473	1	7
β-strand	478	1	7
β-strand	481-486	6	4
β-strand	490-492	3	4
α-helix	494-496	3
α-helix	500-502	3
α-helix	533-535	3
β-strand	538-539	2	8
β-strand	547-548	2	8
β-strand	553-555	3	9
β-strand	562-564	3	9
α-helix	565-566	2
β-strand	567-568	2	10
α-helix	578-600	23
α-helix	605-610	6
α-helix	612-632	21
α-helix	638-671	34
α-helix	674	1
α-helix	681-683	3
α-helix	684-688	5
α-helix	689-709	21
β-strand	714-717	4	10
β-strand	726-730	5	10
α-helix	734-757	24
α-helix	763-791	29
α-helix	792-794	3
α-helix	796-814	19
α-helix	815-819	5
α-helix	820-827	8
β-strand	836	1	11
β-strand	857-862	6	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Metabotropic glutamate receptor 3	B, R	protein	879	Homo sapiens	Q14832 (AlphaFold model)
Beta-arrestin-1	A, C	protein	418	Homo sapiens	P49407 (AlphaFold model)
scFv30	D, S	protein	251	Mus musculus

Sequence of entity 1 (B, R), FASTA

>9II2_1 Metabotropic glutamate receptor 3 (chains B, R)
MKMLTRLQVLTLALFSKGFLLSLGDHNFLRREIKIEGDLVLGGLFPINEKGTGTEECGRI
NEDRGIQRLEAMLFAIDEINKDDYLLPGVKLGVHILDTCSRDTYALEQSLEFVRASLTKV
DEAEYMCPDGSYAIQENIPLLIAGVIGGSYSSVSIQVANLLRLFQIPQISYASTSAKLSD
KSRYDYFARTVPPDFYQAKAMAEILRFFNWTYVSTVASEGDYGETGIEAFEQEARLRNIC
IATAEKVGRSNIRKSYDSVIRELLQKPNARVVVLFMRSDDSRELIAAASRANASFTWVAS
DGWGAQESIIKGSEHVAYGAITLELASQPVRQFDRYFQSLNPYNNHRNPWFRDFWEQKFQ
CSLQNKRNHRRVCDKHLAIDSSNYEQESKIMFVVNAVYAMAHALHKMQRTLCPNTTKLCD
AMKILDGKKLYKDYLLKINFTAPFNPNKDADSIVKFDTFGDGMGRYNVFNFQNVGGKYSY
LKVGHWAETLSLDVNSIHWSRNSVPTSQCSDPCAPNEMKNMQPGDVCCWICIPCEPYEYL
ADEFTCMDCGSGQWPTADLTGCYDLPEDYIRWEDAWAIGPVTIACLGFMCTCMVVTVFIK
HNNTPLVKASGRELCYILLFGVGLSYCMTFFFIAKPSPVICALRRLGLGSSFAICYSALL
TKTNCIARIFDGVKNGAQRPKFISPSSQVFICLGLILVQIVMVSVWLILEAPGTRRYTLA
EKRETVILKCNVKDSSMLISLTYDVILVILCTVYAFKTRKCPENFNEAKFIGFTMYTTCI
IWLAFLPIFYVTSSDYRVQTTTMCISVSLSGFVVLGCLFAPKVHIILFQPQKNVVTHRLH
LNRFSVSGTGTTYSQSSASTYVPTVCNGREVLDSTTSSL

Sequence of entity 2 (A, C), FASTA

>9II2_2 Beta-arrestin-1 (chains A, C)
MGDKGTRVFKKASPNGKLTVYLGKRDFVDHIDLVDPVDGVVLVDPEYLKERRVYVTLTVA
FRYGREDLDVLGLTFRKDLFVANVQSFPPAPEDKKPLTRLQERLIKKLGEHAYPFTFEIP
PNLPSSVTLQPGPEDTGKALGVDYEVKAFVAENLEEKIHKRNSVRLVIEKVQYAPERPGP
QPTAETTRQFLMSDKPLHLEASLDKEIYYHGEPISVNVHVTNNTNKTVKKIKISVRQYAD
IVLFNTAQYKVPVAMEEADDTVAPSSTFSKVYTLTPFLANNREKRGLALDGKLKHEDTNL
ASSTLLREGANREILGIIVSYKVKVKLVVSRGGLLGDLASSDVAVELPFTLMHPKPKEEP
PHREVPENETPVDTNLIELDTNDDDIVFEDFARQRLKGMKDDKEEEEDGTGSPQLNNR

Sequence of entity 3 (D, S), FASTA

>9II2_3 scFv30 (chains D, S)
SDIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVP
SRFSGSRSGTDFTLTISSLQPEDFATYYCQQYKYVPVTFGQGTKVEIKGTTAASGSSGGS
SSGAEVQLVESGGGLVQPGGSLRLSCAASGFNVYSSSIHWVRQAPGKGLEWVASISSYYG
YTYYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARSRQFWYSGLDYWGQGTLV
TVSSAHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
CLR	Cholesterol	C27 H46 O	6
GLU	Glutamic acid	C5 H9 N O4	2

Primary citation

Molecular basis of beta-arrestin coupling to the metabotropic glutamate receptor mGlu3. Wen, T., Du, M., Lu, Y. et al. Nat Chem Biol (2025) 21:1262-1269. DOI 10.1038/s41589-025-01858-8 · PubMed

Other PDB entries of the same protein (UniProt Q14832 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3SM9 2.26 Å, Crystal Structure of Metabotropic glutamate receptor 3 precursor in presence of LY341495…
4XAR 2.26 Å, mGluR2 ECD and mGluR3 ECD complex with ligands
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
6B7H 2.82 Å, Structure of mGluR3 with an agonist
5CNM 2.84 Å, mGluR3 complexed with glutamate analog
8JCY 2.9 Å, Cryo-EM structure of mGlu2-mGlu3 heterodimer in presence of LY341495, NAM563, and…
8JCW 3.0 Å, Cryo-EM structure of mGlu2-mGlu3 heterodimer in presence of LY341495 and NAM563…
8JCX 3.0 Å, Cryo-EM structure of mGlu2-mGlu3 heterodimer in presence of LY341495 and NAM563…
8JCZ 3.0 Å, Cryo-EM structure of mGlu2-mGlu3 heterodimer in presence of LY341495, NAM563, and…
5CNK 3.15 Å, mglur3 with glutamate
8JD0 3.3 Å, Cryo-EM structure of mGlu2-mGlu3 heterodimer in presence of NAM563

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