8JD2: PDB entry 8JD2

Cryo-EM structure of G protein-free mGlu2-mGlu3 heterodimer in Acc state. Determined by electron microscopy at 2.8 Å resolution. Released 21 Jun 2023.

Method: Electron microscopy
Resolution: 2.8 Å
Organism: Homo sapiens
Chains: 2
Atoms: 10,730
Mol. weight: 222.85 kDa
Ligands: NAG, GLU
Released: 21 Jun 2023

Explore 8JD2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8JD2 contains 54 α-helices and 49 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, 22 β-strands

Element	Residues	Length	Sheet
β-strand	26-28	3	1
β-strand	32-38	7	1
β-strand	41-43	3	2
β-strand	50-53	4	2
α-helix	55-59	5
α-helix	60-73	14
β-strand	84-90	7	1
α-helix	95-107	13
β-strand	136-141	6	1
α-helix	145-155	11
β-strand	162-164	3	1
α-helix	170-173	4
β-strand	181-183	3	1
α-helix	188-201	14
β-strand	206-212	7	3
α-helix	216-230	15
β-strand	234-241	8	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	345-352	8
α-helix	376-378	3
α-helix	379-399	21
α-helix	415-418	4
α-helix	419-423	5
β-strand	427-429	3	4
β-strand	440-442	3	4
β-strand	453-460	8	3
β-strand	466-474	9	3
β-strand	478-480	3	3
α-helix	482-484	3
α-helix	490-492	3
β-strand	512	1	5
β-strand	521	1	5
α-helix	569-592	24
α-helix	605-623	19
α-helix	632-656	25
α-helix	678-701	24
β-strand	707	1	6
β-strand	719	1	6
α-helix	722-749	28
α-helix	756-774	19
α-helix	776-783	8
α-helix	791-809	19

Chain 3: 29 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	33-35	3	7
β-strand	39-45	7	7
β-strand	48	1	8
β-strand	60	1	8
α-helix	62-67	6
α-helix	68-80	13
α-helix	90	1
β-strand	91-97	7	7
α-helix	102-114	13
β-strand	142-145	4	7
α-helix	151-161	11
β-strand	168	1	7
β-strand	169-170	2	9
α-helix	176-179	4
β-strand	188-189	2	9
α-helix	194-207	14
β-strand	212-218	7	10
α-helix	223-236	14
β-strand	240-247	8	10
α-helix	253-263	11
β-strand	271-275	5	10
α-helix	278-289	12
β-strand	296-299	4	10
α-helix	314-317	4
β-strand	321-325	5	10
α-helix	331-337	7
α-helix	351-358	8
α-helix	372-373	2
α-helix	388-390	3
α-helix	391-411	21
α-helix	420-422	3
α-helix	427-430	4
α-helix	431-435	5
β-strand	440-441	2	11
α-helix	450-452	3
β-strand	453-454	2	11
β-strand	466-474	9	10
β-strand	477-486	10	10
β-strand	490-492	3	10
α-helix	494-496	3
β-strand	518-521	4	12
β-strand	530-533	4	12
β-strand	539-540	2	13
β-strand	546-547	2	13
β-strand	553-555	3	14
β-strand	562-564	3	14
β-strand	568	1	15
α-helix	575-596	22
α-helix	614-621	8
α-helix	623-632	10
α-helix	640-663	24
α-helix	690-701	12
β-strand	726	1	15
α-helix	735-756	22
α-helix	767-782	16
α-helix	796-826	31

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

>8JD2_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

>8JD2_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
GLU	Glutamic acid	C5 H9 N O4	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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