8JCZ: PDB entry 8JCZ

Cryo-EM structure of mGlu2-mGlu3 heterodimer in presence of LY341495, NAM563, and LY2389575 (dimerization mode III). 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: 10,540
Mol. weight: 223.26 kDa
Ligands: Z99, NAG
Released: 21 Jun 2023

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

Secondary structure: helices and β-sheets

8JCZ contains 59 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: 25 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	25-28	4	1
β-strand	33-38	6	1
β-strand	41-43	3	2
α-helix	44	1
β-strand	50-53	4	2
α-helix	55-59	5
α-helix	60-73	14
β-strand	86-90	5	1
α-helix	95-107	13
β-strand	136-139	4	1
α-helix	145-157	13
β-strand	162-164	3	1
α-helix	170-172	3
β-strand	181-183	3	1
α-helix	189-201	13
β-strand	206-207	2	3
β-strand	210-212	3	4
α-helix	215-230	16
β-strand	234-235	2	3
β-strand	240-241	2	4
α-helix	247-258	12
β-strand	266-269	4	4
α-helix	272-285	14
β-strand	291-293	3	4
β-strand	314-319	6	4
α-helix	325-332	8
α-helix	345-352	8
α-helix	378-399	22
α-helix	415-417	3
α-helix	418-423	6
β-strand	428-429	2	5
α-helix	430	1
β-strand	440-441	2	5
β-strand	453-459	7	4
β-strand	467-474	8	4
β-strand	478	1	4
β-strand	507-513	7	6
β-strand	516-524	9	6
α-helix	525-526	2
β-strand	530-531	2	7
β-strand	537-538	2	7
β-strand	541	1	8
β-strand	543	1	8
α-helix	566-568	3
α-helix	569-593	25
α-helix	604-625	22
α-helix	633-659	27
α-helix	677-700	24
β-strand	707	1	9
β-strand	719	1	9
α-helix	727-749	23
α-helix	756-783	28
α-helix	787-818	32

Chain 3: 34 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	33-35	3	10
β-strand	39-45	7	10
β-strand	48-50	3	11
α-helix	51	1
β-strand	57-60	4	11
α-helix	62-67	6
α-helix	68-81	14
α-helix	89-90	2
β-strand	91-97	7	10
α-helix	102-109	8
β-strand	142-147	6	10
α-helix	151-163	13
β-strand	168-170	3	10
α-helix	176-179	4
β-strand	187-189	3	10
α-helix	192-193	2
α-helix	195-207	13
β-strand	212-217	6	12
β-strand	218	1	13
α-helix	222-236	15
β-strand	240-244	5	12
β-strand	247	1	13
α-helix	253-264	12
β-strand	271-275	5	12
α-helix	278-291	14
β-strand	296-299	4	12
α-helix	307-310	4
α-helix	314-317	4
β-strand	321-325	5	12
α-helix	331-338	8
α-helix	351-358	8
α-helix	388-390	3
α-helix	391-411	21
α-helix	420-422	3
α-helix	427-429	3
α-helix	430-435	6
α-helix	440	1
β-strand	441	1	14
α-helix	442	1
α-helix	445-446	2
β-strand	453	1	14
β-strand	465-474	10	12
β-strand	477-487	11	12
β-strand	490	1	12
α-helix	494-496	3
α-helix	512-514	3
β-strand	539	1	15
β-strand	547	1	15
α-helix	575-597	23
α-helix	613-632	20
α-helix	642-664	23
α-helix	685-707	23
α-helix	721-723	3
α-helix	738-757	20
α-helix	768-791	24
α-helix	797-824	28

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

>8JCZ_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

>8JCZ_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
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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