8JCW: PDB entry 8JCW

Cryo-EM structure of mGlu2-mGlu3 heterodimer in presence of LY341495 and NAM563 (dimerization mode I). Determined by electron microscopy at 3.0 Å resolution. Released 21 Jun 2023.

Method: Electron microscopy
Resolution: 3.0 Å
Organism: Homo sapiens
Chains: 2
Atoms: 10,760
Mol. weight: 224.03 kDa
Ligands: CLR, Z99, NAG
Released: 21 Jun 2023

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

Secondary structure: helices and β-sheets

8JCW contains 58 α-helices and 50 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: 29 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	28	1	1
β-strand	32-38	7	1
β-strand	41	1	2
α-helix	45-47	3
β-strand	53	1	2
α-helix	59-73	15
α-helix	83	1
β-strand	84-90	7	1
α-helix	95-106	12
β-strand	136-141	6	1
α-helix	145-156	12
β-strand	162-164	3	1
α-helix	170-172	3
β-strand	181-183	3	1
α-helix	190-201	12
β-strand	206-211	6	3
α-helix	215-229	15
β-strand	234-240	7	3
α-helix	247-258	12
β-strand	265-269	5	3
α-helix	272-284	13
β-strand	290-293	4	3
β-strand	315-319	5	3
α-helix	325-332	8
α-helix	345-353	9
α-helix	378-399	22
α-helix	415-417	3
α-helix	418-423	6
β-strand	428-429	2	4
α-helix	430	1
β-strand	440-441	2	4
β-strand	453-459	7	3
β-strand	467-474	8	3
β-strand	478-480	3	3
α-helix	503-504	2
β-strand	508-511	4	5
α-helix	512-513	2
β-strand	521-524	4	5
β-strand	529-531	3	6
β-strand	537-539	3	6
α-helix	544	1
β-strand	545	1	7
α-helix	546	1
β-strand	555	1	7
α-helix	556-558	3
α-helix	570-591	22
α-helix	592-594	3
α-helix	603-623	21
α-helix	631-658	28
α-helix	676-700	25
α-helix	725-747	23
α-helix	756-783	28
α-helix	788-817	30

Chain 3: 29 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	33-34	2	8
β-strand	39-45	7	8
β-strand	48-50	3	9
α-helix	51	1
β-strand	57-60	4	9
α-helix	62-66	5
α-helix	67-80	14
α-helix	89-90	2
β-strand	91-97	7	8
α-helix	102-108	7
α-helix	110-113	4
α-helix	114-116	3
β-strand	142-146	5	8
α-helix	151-161	11
β-strand	168-170	3	8
α-helix	176-179	4
β-strand	187-189	3	8
α-helix	195-207	13
β-strand	212-217	6	10
α-helix	222-236	15
β-strand	240-246	7	10
α-helix	255-264	10
β-strand	271-275	5	10
α-helix	280-290	11
β-strand	296-299	4	10
β-strand	321-325	5	10
α-helix	331-338	8
α-helix	351-358	8
β-strand	362	1	11
β-strand	372	1	11
α-helix	390-411	22
α-helix	420-422	3
α-helix	427-434	8
β-strand	440-441	2	12
β-strand	453-454	2	12
α-helix	461-463	3
β-strand	466-473	8	10
β-strand	478-486	9	10
β-strand	490	1	10
β-strand	518-521	4	13
β-strand	530-533	4	13
β-strand	538-539	2	14
β-strand	547-548	2	14
β-strand	554-555	2	15
β-strand	562-563	2	15
α-helix	569-570	2
α-helix	579-600	22
α-helix	612-631	20
α-helix	638-663	26
α-helix	683-706	24
α-helix	718-720	3
α-helix	732-734	3
α-helix	735-755	21
α-helix	765-791	27
α-helix	797-825	29

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

>8JCW_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

>8JCW_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
CLR	Cholesterol	C27 H46 O	2
Z99	2-[(1S,2S)-2-carboxycyclopropyl]-3-(9H-xanthen-9-yl)-D-alanine	C20 H19 N O5	2
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	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

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