8JCV: MGlu2-mGlu3 heterodimer in presence of LY341495

Cryo-EM structure of mGlu2-mGlu3 heterodimer in presence of LY341495 (dimerization mode II). Determined by electron microscopy at 3.4 Å resolution. Released 21 Jun 2023.

Method: Electron microscopy
Resolution: 3.4 Å
Organism: Homo sapiens
Chains: 2
Atoms: 10,667
Mol. weight: 223.2 kDa
Ligands: NAG, Z99
Released: 21 Jun 2023

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

Secondary structure: helices and β-sheets

8JCV contains 63 α-helices and 54 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: 34 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	26-27	2	1
β-strand	32-37	6	1
β-strand	41	1	2
β-strand	53	1	2
α-helix	55-59	5
α-helix	60-74	15
β-strand	84-89	6	1
α-helix	95-102	8
α-helix	103-105	3
β-strand	139	1	3
α-helix	146-158	13
β-strand	162-164	3	3
α-helix	171-173	3
β-strand	181-183	3	3
α-helix	190-201	12
β-strand	206-207	2	4
β-strand	208-210	3	5
α-helix	219-230	12
β-strand	234-235	2	4
β-strand	239	1	5
α-helix	247-259	13
β-strand	265-268	4	5
α-helix	272-284	13
β-strand	290-293	4	5
α-helix	301-304	4
β-strand	315-319	5	5
α-helix	325-331	7
α-helix	345-352	8
α-helix	361-363	3
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	428-429	2	6
α-helix	430	1
β-strand	440-441	2	6
β-strand	443	1	7
α-helix	448	1
β-strand	449	1	7
α-helix	450-451	2
β-strand	453-458	6	5
β-strand	468-474	7	5
β-strand	478-480	3	5
α-helix	482-484	3
β-strand	516	1	8
β-strand	519	1	8
α-helix	524-526	3
β-strand	530	1	9
β-strand	538	1	9
α-helix	545-546	2
α-helix	569-591	23
α-helix	596-600	5
α-helix	603-622	20
α-helix	632-659	28
α-helix	676-701	26
α-helix	724-748	25
α-helix	758-783	26
α-helix	787-817	31

Chain 3: 29 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	32-35	4	10
β-strand	39-45	7	10
β-strand	48-50	3	11
β-strand	57-60	4	11
α-helix	62-67	6
α-helix	68-81	14
β-strand	91-97	7	10
α-helix	102-108	7
α-helix	110-114	5
β-strand	144-147	4	10
α-helix	151-163	13
β-strand	168-170	3	10
α-helix	177-179	3
β-strand	188-189	2	10
α-helix	195-207	13
β-strand	212-218	7	12
α-helix	221-237	17
β-strand	240-247	8	12
α-helix	253-264	12
β-strand	271-275	5	12
α-helix	278-289	12
β-strand	296-298	3	12
β-strand	321-325	5	12
α-helix	331-338	8
α-helix	350-359	10
β-strand	362	1	13
α-helix	371	1
β-strand	372	1	13
α-helix	373-374	2
α-helix	381-383	3
α-helix	390-411	22
α-helix	427-432	6
β-strand	440-441	2	14
α-helix	442	1
β-strand	453-454	2	14
β-strand	456	1	15
α-helix	461	1
β-strand	462	1	15
α-helix	463	1
β-strand	466-474	9	12
β-strand	477-486	10	12
β-strand	490-492	3	12
α-helix	511-513	3
β-strand	518-521	4	16
β-strand	530-533	4	16
α-helix	545-548	4
β-strand	553	1	17
β-strand	564	1	17
β-strand	567	1	18
α-helix	578-600	23
α-helix	614-631	18
α-helix	640-664	25
α-helix	685-705	21
β-strand	726	1	18
α-helix	733-758	26
α-helix	765-790	26
α-helix	798-824	27

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

>8JCV_1 Metabotropic glutamate receptor 2,Peptidyl-prolyl cis-trans isomerase FKBP1A (chains 2)
DYKDDDDGAPEGPAKKVLTLEGDLVLGGLFPVHQKGGPAEDCGPVNEHRGIQRLEAMLFA
LDRINRDPHLLPGVRLGAHILDSCSKDTHALEQALDFVRASLSRGADGSRHICPDGSYAT
HGDAPTAITGVIGGSYSDVSIQVANLLRLFQIPQISYASTSAKLSDKSRYDYFARTVPPD
FFQAKAMAEILRFFNWTYVSTVASEGDYGETGIEAFELEARARNICVATSEKVGRAMSRA
AFEGVVRALLQKPSARVAVLFTRSEDARELLAASQRLNASFTWVASDGWGALESVVAGSE
GAAEGAITIELASYPISDFASYFQSLDPWNNSRNPWFREFWEQRFRCSFRQRDCAAHSLR
AVPFEQESKIMFVVNAVYAMAHALHNMHRALCPNTTRLCDAMRPVNGRRLYKDFVLNVKF
DAPFRPADTHNEVRFDRFGDGIGRYNIFTYLRAGSGRYRYQKVGYWAEGLTLDTSLIPWA
SPSAGPLPASRCSEPCLQNEVKSVQPGEVCCWLCIPCQPYEYRLDEFTCADCGLGYWPNA
SLTGCFALPQEYIRWGDAWAVGPVTIACLGALATLFVLGVFVRHNATPVVKASGRELCYI
LLGGVFLCYCMTFIFIAKPSTAVCTLRRLGLGTAFSVCYSALLTKTNRIARIFGGAREGA
QRPRFISPASQVAICLALISGQLLIVVAWLVVEAPGTGKETAPERREVVTLRCNHRDASM
LGSLAYNVLLIALCTLYAFKTRKCPENFNEAKFIGFTMYTTCIIWLAFLPIFYVTSSDYR
VQTTTMCVSVSLSGSVVLGCLFAPKLHIILFQPQKNVVSHRAPTSRFGSAAARASSSLGQ
GSGSQFVPTVCNGREVVDSTTSSLLEVLFQGPGVQVETISPGDGRTFPKRGQTCVVHYTG
MLEDGKKFDSSRDRNKPFKFMLGKQEVIRGWEEGVAQMSVGQRAKLTISPDYAYGATGHP
GIIPPHATLVFDVELLKLEFAAAHHHHHHHHHH

Sequence of entity 2 (3), FASTA

>8JCV_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
Z99	2-[(1S,2S)-2-carboxycyclopropyl]-3-(9H-xanthen-9-yl)-D-alanine	C20 H19 N O5	2

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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