8JD5: Gi1-bound mGlu2-mGlu4 heterodimer

Cryo-EM structure of Gi1-bound mGlu2-mGlu4 heterodimer. Determined by electron microscopy at 3.6 Å resolution. Released 21 Jun 2023.

Method: Electron microscopy
Resolution: 3.6 Å
Organisms: Homo sapiens, Escherichia coli
Chains: 6
Atoms: 18,028
Mol. weight: 316.65 kDa
Ligands: HZR, GLU, CLR, PEF
Released: 21 Jun 2023

Explore 8JD5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8JD5 contains 83 α-helices and 111 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 2: 34 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	28	1	1
β-strand	33-38	6	2
β-strand	41-43	3	3
β-strand	50-53	4	3
α-helix	54	1
α-helix	59-73	15
β-strand	86	1	1
β-strand	87-90	4	2
α-helix	95-101	7
α-helix	102-106	5
β-strand	136-141	6	2
α-helix	145-157	13
β-strand	162-164	3	2
β-strand	181-183	3	2
α-helix	192-201	10
β-strand	206-212	7	4
α-helix	217-230	14
β-strand	234-235	2	4
β-strand	239-241	3	4
α-helix	247-257	11
β-strand	265-269	5	4
α-helix	272-283	12
β-strand	290-293	4	4
β-strand	314-319	6	4
α-helix	325-332	8
α-helix	345-351	7
α-helix	378-399	22
α-helix	415-422	8
β-strand	428-429	2	5
α-helix	430	1
α-helix	433-434	2
β-strand	440-441	2	5
β-strand	453-459	7	4
β-strand	467-474	8	4
β-strand	478	1	4
α-helix	486-488	3
α-helix	490-492	3
α-helix	495-496	2
β-strand	509-511	3	6
β-strand	522-524	3	6
α-helix	539-540	2
α-helix	566-568	3
α-helix	570-591	22
α-helix	598-600	3
α-helix	603-620	18
α-helix	621-623	3
α-helix	629-661	33
α-helix	670-671	2
α-helix	676-700	25
α-helix	729-746	18
α-helix	754-756	3
α-helix	759-782	24
α-helix	787-805	19
α-helix	806-810	5
α-helix	811-814	4
α-helix	815-819	5

Chain 4: 31 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	45	1	7
β-strand	49-55	7	7
α-helix	70-71	2
α-helix	72-76	5
α-helix	77-89	13
β-strand	101-107	7	7
α-helix	112-119	8
β-strand	150-154	5	7
α-helix	155-156	2
α-helix	159-169	11
β-strand	176-178	3	7
α-helix	185-187	3
β-strand	195-197	3	7
α-helix	202-215	14
β-strand	220-226	7	8
α-helix	231-245	15
β-strand	249-256	8	8
α-helix	262-274	13
β-strand	280-284	5	8
α-helix	287-299	13
β-strand	307-310	4	8
α-helix	312-314	3
α-helix	319-321	3
β-strand	332-336	5	8
α-helix	342-348	7
α-helix	361-371	11
α-helix	395-397	3
α-helix	406-427	22
α-helix	436-438	3
α-helix	443-451	9
β-strand	455-456	2	9
β-strand	462-463	2	9
β-strand	475-481	7	8
β-strand	488-494	7	8
β-strand	531-533	3	10
β-strand	540-542	3	10
β-strand	553	1	11
β-strand	556	1	11
β-strand	564-566	3	12
β-strand	573-575	3	12
α-helix	576-577	2
α-helix	586-588	3
α-helix	590-611	22
α-helix	618-620	3
α-helix	627-643	17
α-helix	649-686	38
α-helix	696-720	25
β-strand	734	1	13
β-strand	740	1	13
α-helix	750-773	24
α-helix	781-783	3
α-helix	785-799	15
α-helix	802-805	4
α-helix	820-846	27

Chain A: 9 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	7-31	25
β-strand	33-34	2	14
β-strand	36-39	4	14
α-helix	47-49	3
β-strand	185-191	7	14
β-strand	194-200	7	14
α-helix	209-212	4
α-helix	213-215	3
β-strand	220-226	7	14
β-strand	233	1	15
β-strand	241	1	15
α-helix	242-255	14
β-strand	263-269	7	14
α-helix	271-280	10
α-helix	283-285	3
α-helix	296-308	13
β-strand	319-322	4	14
α-helix	331-351	21

Chain B: 1 helix, 32 β-strands

Element	Residues	Length	Sheet
α-helix	8-28	21
β-strand	51	1	16
β-strand	58-62	5	17
β-strand	69-74	6	17
β-strand	78-83	6	17
β-strand	91-94	4	17
β-strand	100-105	6	18
β-strand	111-116	6	18
β-strand	122-125	4	18
β-strand	134-135	2	18
β-strand	149-150	2	19
β-strand	156-159	4	19
β-strand	167-170	4	19
β-strand	176-179	4	19
β-strand	190	1	20
β-strand	201	1	20
β-strand	207-209	3	21
β-strand	212	1	22
β-strand	215	1	22
β-strand	221-223	3	21
β-strand	229-232	4	23
β-strand	240-245	6	23
β-strand	250-254	5	23
β-strand	260-264	5	23
β-strand	273	1	24
β-strand	278	1	25
β-strand	284-286	3	25
β-strand	289	1	24
β-strand	293-298	6	25
β-strand	303-309	7	25
β-strand	315-320	6	16
β-strand	327-331	5	16
β-strand	336-339	4	16

Chain C: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	10-24	15
α-helix	32-43	12

Chain H: 6 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	26
β-strand	6-7	2	27
β-strand	20-23	4	27
α-helix	24	1
β-strand	25	1	26
β-strand	33-39	7	28
β-strand	45-51	7	28
α-helix	53-55	3
β-strand	58-60	3	28
α-helix	62-64	3
β-strand	69-73	5	27
β-strand	78-82	5	27
α-helix	88-90	3
β-strand	93-99	7	28
β-strand	110-111	2	28
β-strand	115-116	2	28
α-helix	138-139	2
β-strand	140-141	2	29
β-strand	146	1	30
β-strand	155-161	7	29
β-strand	166	1	31
β-strand	172	1	31
β-strand	174-179	6	30
β-strand	186-190	5	30
β-strand	194-195	2	30
α-helix	196	1
β-strand	204-208	5	29
β-strand	211-216	6	29
β-strand	226-231	6	30
β-strand	239	1	30
β-strand	243-244	2	30

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Metabotropic glutamate receptor 2	2	protein	870	Homo sapiens	Q14416 (AlphaFold model)
Metabotropic glutamate receptor 4	4	protein	916	Homo sapiens	Q14833 (AlphaFold model)
Guanine nucleotide-binding protein G(i) subunit alpha-1	A	protein	354	Homo sapiens	P63096 (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)/G(S)/G(O) subunit gamma-2	C	protein	71	Homo sapiens	P59768
scFv	H	protein	257	Escherichia coli

Sequence of entity 1 (2), FASTA

>8JD5_1 Metabotropic glutamate receptor 2 (chains 2)
DYKDDDDGAPEGPAKKVLTLEGDLVLGGLFPVHQKGGPAEDCGPVNEHRGIQRLEAMLFA
LDRINRDPHLLPGVRLGAHILDSCSKDTHALEQALDFVRASLSRGADGSRHICPDGSYAT
HGDAPTAITGVIGGSYSDVSIQVANLLRLFQIPQISYASTSAKLSDKSRYDYFARTVPPD
FFQAKAMAEILRFFNWTYVSTVASEGDYGETGIEAFELEARARNICVATSEKVGRAMSRA
AFEGVVRALLQKPSARVAVLFTRSEDARELLAASQRLNASFTWVASDGWGALESVVAGSE
GAAEGAITIELASYPISDFASYFQSLDPWNNSRNPWFREFWEQRFRCSFRQRDCAAHSLR
AVPFEQESKIMFVVNAVYAMAHALHNMHRALCPNTTRLCDAMRPVNGRRLYKDFVLNVKF
DAPFRPADTHNEVRFDRFGDGIGRYNIFTYLRAGSGRYRYQKVGYWAEGLTLDTSLIPWA
SPSAGPLPASRCSEPCLQNEVKSVQPGEVCCWLCIPCQPYEYRLDEFTCADCGLGYWPNA
SLTGCFELPQEYIRWGDAWAVGPVTIACLGALATLFVLGVFVRHNATPVVKASGRELCYI
LLGGVFLCYCMTFIFIAKPSTAVCTLRRLGLGTAFSVCYSALLTKTNRIARIFGGAREGA
QRPRFISPASQVAICLALISGQLLIVVAWLVVEAPGTGKETAPERREVVTLRCNHRDASM
LGSLAYNVLLIALCTLYAFKTRKCPENFNEAKFIGFTMYTTCIIWLAFLPIFYVTSSDYR
VQTTTMCVSVSLSGSVVLGCLFAPKLHIILFQPQKNVVSHRAPTSRFGSAAARASSSLGQ
GSGSQFVPTVCNGREVVDSTTSSLLEVLFQ

Sequence of entity 2 (4), FASTA

>8JD5_2 Metabotropic glutamate receptor 4 (chains 4)
DYKDDDDGAPWSHPQFEKGSGSWSHPQFEKKPKGHPHMNSIRIDGDITLGGLFPVHGRGS
EGKPCGELKKEKGIHRLEAMLFALDRINNDPDLLPNITLGARILDTCSRDTHALEQSLTF
VQALIEKDGTEVRCGSGGPPIITKPERVVGVIGASGSSVSIMVANILRLFKIPQISYAST
APDLSDNSRYDFFSRVVPSDTYQAQAMVDIVRALKWNYVSTVASEGSYGESGVEAFIQKS
REDGGVCIAQSVKIPREPKAGEFDKIIRRLLETSNARAVIIFANEDDIRRVLEAARRANQ
TGHFFWMGSDSWGSKIAPVLHLEEVAEGAVTILPKRMSVRGFDRYFSSRTLDNNRRNIWF
AEFWEDNFHCKLSRHALKKGSHVKKCTNRERIGQDSAYEQEGKVQFVIDAVYAMGHALHA
MHRDLCPGRVGLCPRMDPVDGTQLLKYIRNVNFSGIAGNPVTFNENGDAPGRYDIYQYQL
RNDSAEYKVIGSWTDHLHLRIERMHWPGSGQQLPRSICSLPCQPGERKKTVKGMPCCWHC
EPCTGYQYQVDRYTCKTCPYDMRPTENRTGCRPIPIIKLEWGSPWAVLPLFLAVVGIAAT
LFVVITFVRYNDTPIVKASGRELSYVLLAGIFLCYATTFLMIAEPDLGTCSLRRIFLGLG
MSISYAALLTKTNRIYRIFEQGKRSVSAPRFISPASQLAITFSLISLQLLGICVWFVVDP
SHSVVDFQDQRTLDPRFARGVLKCDISDLSLICLLGYSMLLMVTCTVYAIKTRGVPETFN
EAKPIGFTMYTTCIVWLAFIPIFFGTSQSADKLYIQTTTLTVSVSLSASVSLGMLYMPKV
YIILFHPEQNVPKRKRSLKAVVTAATMSNKFTQKGNFRPNGEAKSELCENLEAPALATKQ
TYVTYTNHAILEVLFQ

Sequence of entity 3 (A), FASTA

>8JD5_3 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains A)
MGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKNTIVKQMKIIHEAG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TTGIVETHFTFKDLHFKMFDVGAQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEM
NRMHASMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAA
AYIQCQFEDLNKRKDTKEIYTHFTCSTDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 4 (B), FASTA

>8JD5_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 (C), FASTA

>8JD5_5 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains C)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 6 (H), FASTA

>8JD5_6 scFv (chains H)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLELKAAALEVLFQ

Ligands and cofactors

ID	Name	Formula	Copies
HZR	1-butyl-3-chloranyl-4-(4-phenylpiperidin-1-yl)pyridin-2-one	C20 H25 Cl N2 O	1
GLU	Glutamic acid	C5 H9 N O4	2
CLR	Cholesterol	C27 H46 O	5
PEF	Di-palmitoyl-3-sn-phosphatidylethanolamine	C37 H74 N O8 P	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2
BQI	5-methyl-N-(4-methylpyrimidin-2-yl)-4-(1H-pyrazol-4-yl)-1,3-thiazol-2-amine	C12 H12 N6 S	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 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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