8JD6: Gi1-bound metabotropic glutamate receptor mGlu4

Cryo-EM structure of Gi1-bound metabotropic glutamate receptor mGlu4. Determined by electron microscopy at 3.4 Å resolution. Released 21 Jun 2023.

Method: Electron microscopy
Resolution: 3.4 Å
Organisms: Homo sapiens, Escherichia coli
Chains: 6
Atoms: 17,192
Mol. weight: 314.09 kDa
Ligands: SEP, BK0
Released: 21 Jun 2023

Explore 8JD6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8JD6 contains 65 α-helices and 122 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.

Chain A: 10 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	7-32	26
β-strand	34-40	7	39
α-helix	46-49	4
β-strand	186-190	5	39
β-strand	195-199	5	39
α-helix	208-211	4
α-helix	212-215	4
β-strand	220-226	7	39
α-helix	242-253	12
β-strand	264-269	6	39
α-helix	271-278	8
α-helix	283-285	3
α-helix	296-307	12
β-strand	319-323	5	39
α-helix	330-349	20
α-helix	350-352	3

Chain B: 0 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	47-51	5	31
β-strand	60-63	4	32
β-strand	70-73	4	32
β-strand	78-82	5	32
β-strand	91-94	4	32
β-strand	103-105	3	33
β-strand	111-114	4	33
β-strand	116	1	34
β-strand	121-125	5	33
β-strand	134-139	6	33
β-strand	146-148	3	34
β-strand	151	1	35
β-strand	156-157	2	35
β-strand	160-161	2	34
β-strand	166	1	34
β-strand	168-170	3	35
β-strand	176-178	3	35
β-strand	187-191	5	36
β-strand	199-203	5	36
β-strand	209-211	3	36
β-strand	220-221	2	36
β-strand	229-234	6	37
β-strand	240-245	6	37
β-strand	251-254	4	37
β-strand	260	1	37
β-strand	273-278	6	38
β-strand	284-289	6	38
β-strand	294-298	5	38
β-strand	307	1	38
β-strand	315-320	6	31
β-strand	327-331	5	31
β-strand	336-339	4	31

Chain C: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	30-35	6

Chain D: 2 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	19
β-strand	21-25	5	19
β-strand	33-35	3	20
β-strand	38-39	2	21
β-strand	45-46	2	21
β-strand	49	1	22
β-strand	50-51	2	20
α-helix	53-55	3
β-strand	60	1	22
β-strand	71	1	23
β-strand	80	1	23
α-helix	88-90	3
β-strand	92-94	3	21
β-strand	97-99	3	20
β-strand	111	1	20
β-strand	115-117	3	21
β-strand	159-160	2	24
β-strand	166	1	25
β-strand	172	1	25
β-strand	174-176	3	26
β-strand	177-179	3	27
β-strand	185-187	3	27
β-strand	189-190	2	28
β-strand	194-195	2	28
β-strand	204	1	29
β-strand	211-212	2	24
β-strand	215	1	29
β-strand	225	1	30
β-strand	226	1	27
β-strand	229-231	3	26
β-strand	238	1	26
β-strand	245	1	30

Chain R: 23 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	43-45	3	11
β-strand	49-55	7	11
β-strand	58-60	3	12
β-strand	67-70	4	12
α-helix	72-76	5
α-helix	77-91	15
β-strand	101-107	7	11
α-helix	112-126	15
β-strand	152-154	3	11
α-helix	159-169	11
β-strand	176-178	3	11
α-helix	184-187	4
β-strand	195-197	3	11
α-helix	202-215	14
β-strand	220-226	7	13
α-helix	231-243	13
β-strand	249-256	8	13
α-helix	264-274	11
β-strand	280-283	4	13
α-helix	287-300	14
β-strand	307-310	4	13
β-strand	331-336	6	13
α-helix	342-349	8
α-helix	360-366	7
α-helix	406-427	22
α-helix	436-438	3
α-helix	443-451	9
β-strand	454-455	2	14
β-strand	463-464	2	14
β-strand	475-481	7	13
β-strand	488-495	8	13
β-strand	499	1	13
α-helix	503-505	3
β-strand	530-532	3	15
β-strand	541-543	3	15
β-strand	549-550	2	16
β-strand	558-559	2	16
β-strand	565-566	2	17
β-strand	573-574	2	17
α-helix	589-611	23
α-helix	616-620	5
α-helix	624-644	21
α-helix	649-684	36
α-helix	696-720	25
β-strand	733	1	18
β-strand	741	1	18
α-helix	750-773	24
α-helix	785-807	23
α-helix	814-847	34

Chain S: 29 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	45	1	1
β-strand	49	1	2
β-strand	50-55	6	3
α-helix	68-70	3
α-helix	72-76	5
α-helix	77-91	15
β-strand	101	1	2
β-strand	103	1	1
β-strand	105-107	3	3
α-helix	112-123	12
β-strand	150-154	5	3
α-helix	155-156	2
α-helix	159-171	13
β-strand	176-177	2	3
α-helix	184-186	3
α-helix	202-215	14
β-strand	220-226	7	4
α-helix	229-244	16
β-strand	249-256	8	4
α-helix	265-273	9
β-strand	280-283	4	4
α-helix	287-299	13
β-strand	307-310	4	4
α-helix	312-314	3
β-strand	331-336	6	4
α-helix	342-348	7
α-helix	362-369	8
α-helix	406-426	21
α-helix	436-438	3
α-helix	443-451	9
β-strand	455-456	2	5
β-strand	462-463	2	5
α-helix	471-473	3
β-strand	475-480	6	4
β-strand	493-495	3	4
β-strand	499	1	4
α-helix	503-505	3
β-strand	530-532	3	6
β-strand	541-543	3	6
β-strand	550-551	2	7
β-strand	557-558	2	7
β-strand	564	1	8
α-helix	574	1
β-strand	575	1	8
α-helix	576-577	2
β-strand	578-579	2	9
α-helix	589-611	23
α-helix	624-643	20
α-helix	649-682	34
α-helix	696-718	23
β-strand	726	1	10
β-strand	742-743	2	9
β-strand	745	1	10
α-helix	750-774	25
α-helix	785-807	23
α-helix	818-837	20
α-helix	839-847	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Metabotropic glutamate receptor 4	R, S	protein	890	Homo sapiens	Q14833 (AlphaFold model)
scFv	D	protein	257	Escherichia coli
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	C	protein	71	Homo sapiens	P59768 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	351	Homo sapiens	P62873 (AlphaFold model)
Guanine nucleotide-binding protein G(i) subunit alpha-3	A	protein	354	Homo sapiens	P08754 (AlphaFold model)

Sequence of entity 1 (R, S), FASTA

>8JD6_1 Metabotropic glutamate receptor 4 (chains R, S)
DYKDDDDGAPKPKGHPHMNSIRIDGDITLGGLFPVHGRGSEGKPCGELKKEKGIHRLEAM
LFALDRINNDPDLLPNITLGARILDTCSRDTHALEQSLTFVQALIEKDGTEVRCGSGGPP
IITKPERVVGVIGASGSSVSIMVANILRLFKIPQISYASTAPDLSDNSRYDFFSRVVPSD
TYQAQAMVDIVRALKWNYVSTVASEGSYGESGVEAFIQKSREDGGVCIAQSVKIPREPKA
GEFDKIIRRLLETSNARAVIIFANEDDIRRVLEAARRANQTGHFFWMGSDSWGSKIAPVL
HLEEVAEGAVTILPKRMSVRGFDRYFSSRTLDNNRRNIWFAEFWEDNFHCKLSRHALKKG
SHVKKCTNRERIGQDSAYEQEGKVQFVIDAVYAMGHALHAMHRDLCPGRVGLCPRMDPVD
GTQLLKYIRNVNFSGIAGNPVTFNENGDAPGRYDIYQYQLRNDSAEYKVIGSWTDHLHLR
IERMHWPGSGQQLPRSICSLPCQPGERKKTVKGMPCCWHCEPCTGYQYQVDRYTCKTCPY
DMRPTENRTGCRPIPIIKLEWGSPWAVLPLFLAVVGIAATLFVVITFVRYNDTPIVKASG
RELSYVLLAGIFLCYATTFLMIAEPDLGTCSLRRIFLGLGMSISYAALLTKTNRIYRIFE
QGKRSVSAPRFISPASQLAITFSLISLQLLGICVWFVVDPSHSVVDFQDQRTLDPRFARG
VLKCDISDLSLICLLGYSMLLMVTCTVYAIKTRGVPETFNEAKPIGFTMYTTCIVWLAFI
PIFFGTSQSADKLYIQTTTLTVSVSLSASVSLGMLYMPKVYIILFHPEQNVPKRKRSLKA
VVTAATMSNKFTQKGNFRPNGEAKSELCENLEAPALATKQTYVTYTNHAI

Sequence of entity 2 (D), FASTA

>8JD6_2 scFv (chains D)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLELKAAALEVLFQ

Sequence of entity 3 (C), FASTA

>8JD6_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains C)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 4 (B), FASTA

>8JD6_4 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
MHHHHHHGSLLQSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRR
TLRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSG
NYVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALW
DIETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDI
NAICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGY
DDFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 5 (A), FASTA

>8JD6_5 Guanine nucleotide-binding protein G(i) subunit alpha-3 (chains A)
MGCTLSAEDKAAVERSKMIDRNLREDGEKAAKEVKLLLLGAGESGKNTIVKQMKIIHEDG
YSEDECKQYKVVVYSNTIQSIIAIIRAMGRLKIDFGEAARADDARQLFVLAGSAEEGVMT
PELAGVIKRLWRDGGVQACFSRSREYQLNDSASYYLNDLDRISQSNYIPTQQDVLRTRVK
TTGIVETHFTDKDLYFKMFDVGAQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEM
NRMHASMKLFDSICNNKWFTETSIILFLNKKDLFEEKIKRSPLTICYPEYTGSNTYEEAA
AYIQCQFEDLNRRKDTKEIYTHFTCSTDTKNVQFVFDAVTDVIIKNNLKECGLY

Ligands and cofactors

ID	Name	Formula	Copies
SEP	Phosphoserine	C3 H8 N O6 P	2
BK0	N-(3-chlorophenyl)pyridine-2-carboxamide	C12 H9 Cl N2 O	1

Primary citation

Structural insights into dimerization and activation of the mGlu2-mGlu3 and mGlu2-mGlu4 heterodimers. Wang, X., Wang, M., Xu, T. et al. Cell Res (2023) 33:762-774. DOI 10.1038/s41422-023-00830-2 · PubMed

Other PDB entries of the same protein (UniProt Q14833 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8JD4 2.9 Å, Cryo-EM structure of G protein-free mGlu2-mGlu4 heterodimer in Acc state
8JD5 3.6 Å, Cryo-EM structure of Gi1-bound mGlu2-mGlu4 heterodimer
8WGB 3.7 Å, mGlu2-4 heterodimer bound with Gi
7E9H 4.0 Å, Cryo-EM structure of Gi-bound metabotropic glutamate receptor mGlu4
8WGD 4.45 Å, mGlu2-4 inactive heterodimer
8WG9 4.46 Å, mGlu2-mGlu4 heterodimer bound mGlu4 agonist E7P
8WGC 5.95 Å, heterodimer of mGlu2 and mGlu4 bound with mGlu2 agonist LY379268

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