8JD4: PDB entry 8JD4

Cryo-EM structure of G protein-free mGlu2-mGlu4 heterodimer in Acc state. Determined by electron microscopy at 2.9 Å resolution. Released 21 Jun 2023.

Method: Electron microscopy
Resolution: 2.9 Å
Organism: Homo sapiens
Chains: 2
Atoms: 10,674
Mol. weight: 224.54 kDa
Ligands: NAG, GLU
Released: 21 Jun 2023

Explore 8JD4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8JD4 contains 61 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	25-28	4	1
β-strand	32-37	6	1
β-strand	41-43	3	2
β-strand	50-53	4	2
α-helix	54	1
α-helix	55-60	6
α-helix	61-74	14
β-strand	84-89	6	1
α-helix	95-105	11
β-strand	136-141	6	1
α-helix	145-158	14
β-strand	162-164	3	1
α-helix	170-173	4
β-strand	181-183	3	1
α-helix	188-201	14
β-strand	207-212	6	3
α-helix	217-230	14
β-strand	235-241	7	3
α-helix	247-257	11
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	378-399	22
α-helix	408-410	3
α-helix	415-424	10
β-strand	428-429	2	4
α-helix	430	1
β-strand	440-441	2	4
β-strand	452-458	7	3
β-strand	468-475	8	3
β-strand	478	1	3
α-helix	482-484	3
α-helix	490-492	3
β-strand	510-511	2	5
β-strand	522-523	2	5
α-helix	524-526	3
β-strand	530	1	6
β-strand	538	1	6
β-strand	545	1	7
β-strand	555	1	7
α-helix	569-591	23
α-helix	603-625	23
α-helix	629-654	26
α-helix	679-699	21
α-helix	708-710	3
α-helix	727-749	23
α-helix	759-782	24
α-helix	787-808	22
α-helix	811-814	4
α-helix	815-819	5

Chain 4: 32 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	43-45	3	8
β-strand	49-55	7	8
β-strand	58-60	3	9
α-helix	61	1
β-strand	67-70	4	9
α-helix	76-89	14
β-strand	101-107	7	8
α-helix	112-119	8
α-helix	121-124	4
β-strand	150-155	6	8
α-helix	159-169	11
α-helix	170-172	3
β-strand	176-178	3	8
α-helix	184-187	4
β-strand	195-197	3	8
α-helix	202-215	14
β-strand	220-226	7	10
α-helix	231-245	15
β-strand	249-256	8	10
α-helix	264-274	11
β-strand	280-283	4	10
α-helix	287-299	13
β-strand	307-310	4	10
α-helix	312-314	3
β-strand	332-336	5	10
α-helix	342-349	8
α-helix	362-370	9
β-strand	373	1	11
β-strand	387	1	11
α-helix	394-397	4
α-helix	406-427	22
α-helix	443-450	8
β-strand	456	1	12
α-helix	458-460	3
β-strand	462	1	12
β-strand	475-481	7	10
β-strand	488-495	8	10
β-strand	499	1	10
α-helix	503-505	3
β-strand	529-533	5	13
β-strand	540-544	5	13
α-helix	545-546	2
β-strand	549-550	2	14
β-strand	558-559	2	14
α-helix	560-561	2
β-strand	564-566	3	15
α-helix	567	1
β-strand	573-575	3	15
α-helix	589-611	23
α-helix	615-621	7
α-helix	625-643	19
α-helix	649-653	5
α-helix	655-681	27
α-helix	695-720	26
α-helix	750-774	25
α-helix	781-799	19
α-helix	801-807	7
α-helix	815-847	33

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 4,Serine/threonine-protein kinase mTOR	4	protein	1013	Homo sapiens	A0A8V8TRG9, Q14833 (AlphaFold model)

Sequence of entity 1 (2), FASTA

>8JD4_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 (4), FASTA

>8JD4_2 Metabotropic glutamate receptor 4,Serine/threonine-protein kinase mTOR (chains 4)
DYKDDDDGAPWSHPQFEKGSGSWSHPQFEKKPKGHPHMNSIRIDGDITLGGLFPVHGRGS
EGKPCGELKKEKGIHRLEAMLFALDRINNDPDLLPNITLGARILDTCSRDTHALEQSLTF
VQALIEKDGTEVRCGSGGPPIITKPERVVGVIGASGSSVSIMVANILRLFKIPQISYAST
APDLSDNSRYDFFSRVVPSDTYQAQAMVDIVRALKWNYVSTVASEGSYGESGVEAFIQKS
REDGGVCIAQSVKIPREPKAGEFDKIIRRLLETSNARAVIIFANEDDIRRVLEAARRANQ
TGHFFWMGSDSWGSKIAPVLHLEEVAEGAVTILPKRMSVRGFDRYFSSRTLDNNRRNIWF
AEFWEDNFHCKLSRHALKKGSHVKKCTNRERIGQDSAYEQEGKVQFVIDAVYAMGHALHA
MHRDLCPGRVGLCPRMDPVDGTQLLKYIRNVNFSGIAGNPVTFNENGDAPGRYDIYQYQL
RNDSAEYKVIGSWTDHLHLRIERMHWPGSGQQLPRSICSLPCQPGERKKTVKGMPCCWHC
EPCTGYQYQVDRYTCKTCPYDMRPTENRTGCRPIPIIKLEWGSPWAVLPLFLAVVGIAAT
LFVVITFVRYNDTPIVKASGRELSYVLLAGIFLCYATTFLMIAEPDLGTCSLRRIFLGLG
MSISYAALLTKTNRIYRIFEQGKRSVSAPRFISPASQLAITFSLISLQLLGICVWFVVDP
SHSVVDFQDQRTLDPRFARGVLKCDISDLSLICLLGYSMLLMVTCTVYAIKTRGVPETFN
EAKPIGFTMYTTCIVWLAFIPIFFGTSQSADKLYIQTTTLTVSVSLSASVSLGMLYMPKV
YIILFHPEQNVPKRKRSLKAVVTAATMSNKFTQKGNFRPNGEAKSELCENLEAPALATKQ
TYVTYTNHAILEVLFQGPAILWHEMWHEGLEEASRLYFGERNVKGMFEVLEPLHAMMERG
PQTLKETSFNQAYGRDLMEAQEWCRKYMKSGNVKDLTQAWDLYYHVFRRISKQ

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	3
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

About this viewer

MolViewer shows 8JD4 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.