8JD0: MGlu2-mGlu3 heterodimer in presence of NAM563

Cryo-EM structure of mGlu2-mGlu3 heterodimer in presence of NAM563. Determined by electron microscopy at 3.3 Å resolution. Released 21 Jun 2023.

Method: Electron microscopy
Resolution: 3.3 Å
Organism: Homo sapiens
Chains: 2
Atoms: 11,264
Mol. weight: 226.6 kDa
Ligands: NAG, J9R, CLR, GLU
Released: 21 Jun 2023

Explore 8JD0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8JD0 contains 63 α-helices and 51 β-strands across 2 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: 32 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	32-38	7	1
β-strand	41	1	2
β-strand	53	1	2
α-helix	54	1
α-helix	60-73	14
β-strand	84-90	7	1
α-helix	95-109	15
β-strand	136-139	4	1
α-helix	145-156	12
β-strand	162-164	3	1
α-helix	171-173	3
β-strand	181-183	3	1
α-helix	186-187	2
α-helix	188-190	3
α-helix	191-201	11
β-strand	206-211	6	3
α-helix	215-230	16
β-strand	234-240	7	3
α-helix	247-258	12
β-strand	265-268	4	3
α-helix	272-285	14
β-strand	292	1	3
α-helix	295-297	3
α-helix	301-304	4
β-strand	315-319	5	3
α-helix	327-332	6
α-helix	345-352	8
α-helix	376-378	3
α-helix	379-399	21
α-helix	408-410	3
α-helix	415-417	3
α-helix	418-422	5
α-helix	423-425	3
β-strand	428	1	4
α-helix	429-430	2
β-strand	441	1	4
β-strand	443	1	5
β-strand	448	1	1
β-strand	449	1	5
β-strand	453-459	7	3
β-strand	467-474	8	3
β-strand	478	1	3
α-helix	517-519	3
β-strand	530	1	6
β-strand	540	1	6
β-strand	546	1	7
β-strand	555	1	7
α-helix	565-567	3
α-helix	569-591	23
α-helix	595-599	5
α-helix	603-622	20
α-helix	629-660	32
α-helix	679-699	21
β-strand	705	1	8
β-strand	721	1	8
α-helix	725-747	23
α-helix	756-782	27
α-helix	788-819	32

Chain 3: 31 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	33-34	2	9
β-strand	39-45	7	9
β-strand	48-49	2	10
β-strand	59-60	2	10
α-helix	66-80	15
α-helix	90	1
β-strand	91-97	7	9
α-helix	102-108	7
α-helix	109-112	4
α-helix	114-116	3
β-strand	142-146	5	9
α-helix	147-148	2
α-helix	151-164	14
β-strand	168-170	3	9
β-strand	188-189	2	9
α-helix	194-207	14
β-strand	212-218	7	11
α-helix	221-236	16
β-strand	240-247	8	11
α-helix	255-264	10
β-strand	271-275	5	11
α-helix	278-290	13
β-strand	296-299	4	11
β-strand	321-325	5	11
α-helix	328-330	3
α-helix	331-338	8
α-helix	351-358	8
β-strand	362	1	12
β-strand	372	1	12
α-helix	388-390	3
α-helix	391-411	21
α-helix	427-429	3
α-helix	430-435	6
β-strand	440-441	2	13
β-strand	453-454	2	13
β-strand	466-474	9	11
β-strand	477-485	9	11
β-strand	518-519	2	14
β-strand	532-533	2	14
β-strand	554-555	2	15
β-strand	562-563	2	15
α-helix	564-567	4
α-helix	578-602	25
α-helix	612-633	22
α-helix	638-663	26
α-helix	683-700	18
α-helix	701-705	5
α-helix	706-708	3
β-strand	715	1	16
β-strand	725	1	16
α-helix	729-754	26
α-helix	762-764	3
α-helix	765-790	26
α-helix	799-803	5
α-helix	805-818	14
α-helix	820-827	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Metabotropic glutamate receptor 2,Peptidyl-prolyl cis-trans isomerase FKBP1A	2	protein	993	Homo sapiens	P62942 (AlphaFold model), Q14416 (AlphaFold model)
Metabotropic glutamate receptor 3,Serine/threonine-protein kinase mTOR	3	protein	993	Homo sapiens	A0A8V8TRG9, Q14832 (AlphaFold model)

Sequence of entity 1 (2), FASTA

>8JD0_1 Metabotropic glutamate receptor 2,Peptidyl-prolyl cis-trans isomerase FKBP1A (chains 2)
DYKDDDDGAPEGPAKKVLTLEGDLVLGGLFPVHQKGGPAEDCGPVNEHRGIQRLEAMLFA
LDRINRDPHLLPGVRLGAHILDSCSKDTHALEQALDFVRASLSRGADGSRHICPDGSYAT
HGDAPTAITGVIGGSYSDVSIQVANLLRLFQIPQISYASTSAKLSDKSRYDYFARTVPPD
FFQAKAMAEILRFFNWTYVSTVASEGDYGETGIEAFELEARARNICVATSEKVGRAMSRA
AFEGVVRALLQKPSARVAVLFTRSEDARELLAASQRLNASFTWVASDGWGALESVVAGSE
GAAEGAITIELASYPISDFASYFQSLDPWNNSRNPWFREFWEQRFRCSFRQRDCAAHSLR
AVPFEQESKIMFVVNAVYAMAHALHNMHRALCPNTTRLCDAMRPVNGRRLYKDFVLNVKF
DAPFRPADTHNEVRFDRFGDGIGRYNIFTYLRAGSGRYRYQKVGYWAEGLTLDTSLIPWA
SPSAGPLPASRCSEPCLQNEVKSVQPGEVCCWLCIPCQPYEYRLDEFTCADCGLGYWPNA
SLTGCFELPQEYIRWGDAWAVGPVTIACLGALATLFVLGVFVRHNATPVVKASGRELCYI
LLGGVFLCYCMTFIFIAKPSTAVCTLRRLGLGTAFSVCYSALLTKTNRIARIFGGAREGA
QRPRFISPASQVAICLALISGQLLIVVAWLVVEAPGTGKETAPERREVVTLRCNHRDASM
LGSLAYNVLLIALCTLYAFKTRKCPENFNEAKFIGFTMYTTCIIWLAFLPIFYVTSSDYR
VQTTTMCVSVSLSGSVVLGCLFAPKLHIILFQPQKNVVSHRAPTSRFGSAAARASSSLGQ
GSGSQFVPTVCNGREVVDSTTSSLLEVLFQGPGVQVETISPGDGRTFPKRGQTCVVHYTG
MLEDGKKFDSSRDRNKPFKFMLGKQEVIRGWEEGVAQMSVGQRAKLTISPDYAYGATGHP
GIIPPHATLVFDVELLKLEFAAAHHHHHHHHHH

Sequence of entity 2 (3), FASTA

>8JD0_2 Metabotropic glutamate receptor 3,Serine/threonine-protein kinase mTOR (chains 3)
DYKDDDDKGAPWSHPQFEKGSGSWSHPQFEKLGDHNFLRREIKIEGDLVLGGLFPINEKG
TGTEECGRINEDRGIQRLEAMLFAIDEINKDDYLLPGVKLGVHILDTCSRDTYALEQSLE
FVRASLTKVDEAEYMCPDGSYAIQENIPLLIAGVIGGSYSSVSIQVANLLRLFQIPQISY
ASTSAKLSDKSRYDYFARTVPPDFYQAKAMAEILRFFNWTYVSTVASEGDYGETGIEAFE
QEARLRNICIATAEKVGRSNIRKSYDSVIRELLQKPNARVVVLFMRSDDSRELIAAASRA
NASFTWVASDGWGAQESIIKGSEHVAYGAITLELASQPVRQFDRYFQSLNPYNNHRNPWF
RDFWEQKFQCSLQNKRNHRRVCDKHLAIDSSNYEQESKIMFVVNAVYAMAHALHKMQRTL
CPNTTKLCDAMKILDGKKLYKDYLLKINFTAPFNPNKDADSIVKFDTFGDGMGRYNVFNF
QNVGGKYSYLKVGHWAETLSLDVNSIHWSRNSVPTSQCSDPCAPNEMKNMQPGDVCCWIC
IPCEPYEYLADEFTCMDCGSGQWPTADLTGCYDLPEDYIRWEDAWAIGPVTIACLGFMCT
CMVVTVFIKHNNTPLVKASGRELCYILLFGVGLSYCMTFFFIAKPSPVICALRRLGLGSS
FAICYSALLTKTNCIARIFDGVKNGAQRPKFISPSSQVFICLGLILVQIVMVSVWLILEA
PGTRRYTLAEKRETVILKCNVKDSSMLISLTYDVILVILCTVYAFKTRKCPENFNEAKFI
GFTMYTTCIIWLAFLPIFYVTSSDYRVQTTTMCISVSLSGFVVLGCLFAPKVHIILFQPQ
KNVVTHRLHLNRFSVSGTGTTYSQSSASTYVPTVCNGREVLDSTTSSLLEVLFQGPAILW
HEMWHEGLEEASRLYFGERNVKGMFEVLEPLHAMMERGPQTLKETSFNQAYGRDLMEAQE
WCRKYMKSGNVKDLTQAWDLYYHVFRRISKQEF

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2
J9R	4-(1-methylpyrazol-4-yl)-7-[[(2~{S})-2-(trifluoromethyl)morpholin-4-yl]methyl]q…	C20 H20 F3 N5 O2	1
CLR	Cholesterol	C27 H46 O	9
GLU	Glutamic acid	C5 H9 N O4	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 P62942 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2PPN 0.92 Å, Crystal structure of FKBP12
2PPP 0.94 Å, Crystal structure of E60Q mutant of FKBP12
6YF3 1.0 Å, FKBP12 in complex with the BMP potentiator compound 10 at 1.00A resolution
6YF2 1.03 Å, FKBP12 in complex with the BMP potentiator compound 6 at 1.03A resolution
8X6P 1.05 Å, Isomerase Protein
6YF1 1.12 Å, FKBP12 in complex with the BMP potentiator compound 8 at 1.12A resolution
8CHM 1.12 Å, Human FKBP12 in complex with (1S,5S,6R)-10-((S)-(3,5-dichlorophenyl)sulfinyl)-3-(pyridin-…
4N19 1.2 Å, Structural basis of conformational transitions in the active site and 80 s loop in the…
8PDF 1.2 Å, FKBP12 in complex with PROTAC 6a2
9LYG 1.26 Å, Crystal structure of FKBP12 complexed with Small Molecule Anchor for Protein-201
2PPO 1.29 Å, Crystal structure of E60A mutant of FKBP12
7U8D 1.39 Å, FKBP12 mutant V55G bound to Rapa*-3Z

Browse structure collections

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