8T6J: CDPPB-bound inactive mGlu5

CDPPB-bound inactive mGlu5. Determined by electron microscopy at 3.5 Å resolution. Released 11 Oct 2023.

Method: Electron microscopy
Resolution: 3.5 Å
Organism: Homo sapiens
Chains: 2
Atoms: 11,670
Mol. weight: 198.47 kDa
Ligands: YKU
Released: 11 Oct 2023

Explore 8T6J in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8T6J contains 75 α-helices and 71 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 A: 38 helices, 35 β-strands

Element	Residues	Length	Sheet
β-strand	29-31	3	15
β-strand	35	1	16
β-strand	36-41	6	15
β-strand	44	1	17
α-helix	45-48	4
α-helix	49-51	3
β-strand	60	1	17
α-helix	61	1
α-helix	67-81	15
β-strand	91	1	16
β-strand	93-97	5	15
α-helix	102-116	15
α-helix	141-142	2
β-strand	143-147	5	15
α-helix	154-162	9
α-helix	163-165	3
β-strand	169-171	3	15
α-helix	178-180	3
β-strand	188-190	3	15
α-helix	198-208	11
β-strand	213-216	4	18
β-strand	217	1	19
β-strand	219	1	20
α-helix	222-235	14
α-helix	236-238	3
β-strand	241-245	5	18
β-strand	248	1	20
α-helix	254-265	12
β-strand	274-276	3	19
α-helix	282-293	12
β-strand	301-303	3	19
α-helix	311-313	3
β-strand	325-329	5	19
α-helix	332-334	3
α-helix	335-341	7
α-helix	346-348	3
α-helix	355-363	9
β-strand	366	1	21
β-strand	380	1	21
α-helix	397-418	22
α-helix	427-429	3
α-helix	434-442	9
β-strand	445-447	3	22
β-strand	453-455	3	22
β-strand	466-470	5	19
β-strand	471-475	5	23
β-strand	478-481	4	23
β-strand	485-487	3	19
β-strand	492-494	3	19
α-helix	496-499	4
α-helix	503-505	3
β-strand	520-522	3	24
β-strand	533-535	3	24
α-helix	536-538	3
β-strand	541-543	3	25
β-strand	549-551	3	25
α-helix	552-553	2
β-strand	556-558	3	26
β-strand	565-567	3	26
α-helix	568-570	3
α-helix	578-603	26
α-helix	608-612	5
α-helix	615-629	15
α-helix	632-636	5
α-helix	638-639	2
α-helix	641-672	32
α-helix	690-714	25
β-strand	719-722	4	27
β-strand	730-733	4	27
α-helix	738-760	23
α-helix	766-787	22
α-helix	798-815	18
α-helix	819-826	8

Chain B: 37 helices, 36 β-strands

Element	Residues	Length	Sheet
β-strand	29-31	3	1
β-strand	35	1	2
β-strand	36-41	6	1
β-strand	44	1	3
α-helix	45-48	4
α-helix	49-51	3
β-strand	60	1	3
α-helix	61	1
α-helix	63-67	5
α-helix	68-81	14
β-strand	91	1	2
β-strand	93-97	5	1
α-helix	102-116	15
α-helix	141-142	2
β-strand	143-147	5	1
α-helix	154-162	9
α-helix	163-165	3
β-strand	169-171	3	1
α-helix	178-180	3
β-strand	188-190	3	1
α-helix	198-208	11
β-strand	213-216	4	4
β-strand	217	1	5
β-strand	219	1	6
α-helix	222-236	15
β-strand	241-245	5	4
β-strand	248	1	6
α-helix	254-264	11
α-helix	265-267	3
β-strand	273-276	4	5
α-helix	282-293	12
β-strand	300-303	4	5
β-strand	325-326	2	5
β-strand	327-329	3	7
α-helix	335-341	7
α-helix	346-348	3
α-helix	355-363	9
β-strand	366	1	8
β-strand	380	1	8
α-helix	381-382	2
α-helix	397-418	22
α-helix	434-442	9
β-strand	445-447	3	9
β-strand	453-455	3	9
β-strand	466-468	3	7
β-strand	471-475	5	10
β-strand	478-481	4	10
β-strand	485-487	3	7
β-strand	492-494	3	7
α-helix	496-499	4
α-helix	503-505	3
β-strand	520-522	3	11
β-strand	533-535	3	11
α-helix	536-538	3
β-strand	541-543	3	12
β-strand	549-551	3	12
α-helix	552-553	2
β-strand	556-558	3	13
β-strand	565-567	3	13
α-helix	568-570	3
α-helix	578-603	26
α-helix	608-612	5
α-helix	615-629	15
α-helix	632-636	5
α-helix	638-639	2
α-helix	641-672	32
α-helix	690-714	25
β-strand	719-722	4	14
β-strand	730-733	4	14
α-helix	738-760	23
α-helix	766-792	27
α-helix	798-815	18
α-helix	819-826	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Metabotropic glutamate receptor 5	A, B	protein	881	Homo sapiens	P41594 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>8T6J_1 Metabotropic glutamate receptor 5 (chains A, B)
MKTIIALSYIFCLVFADYKDDDDAAQSSERRVVAHMPGDIIIGALFSVHHQPTVDKVHER
KCGAVREQYGIQRVEAMLHTLERINSDPTLLPNITLGCEIRDSCWHSAVALEQSIEFIRD
SLISSEEEEGLVRCVDGSSSSFRSKKPIVGVIGPGSSSVAIQVQNLLQLFNIPQIAYSAT
SMDLSDKTLFKYFMRVVPSDAQQARAMVDIVKRYNWTYVSAVHTEGNYGESGMEAFKDMS
AKEGICIAHSYKIYSNAGEQSFDKLLKKLTSHLPKARVVACFCEGMTVRGLLMAMRRLGL
AGEFLLLGSDGWADRYDVTDGYQREAVGGITIKLQSPDVKWFDDYYLKLRPETNHRNPWF
QEFWQHRFQCRLEGFPQENSKYNKTCNSSLTLKTHHVQDSKMGFVINAIYSMAYGLHNMQ
MSLCPGYAGLCDAMKPIDGRKLLESLMKTNFTGVSGDTILFDENGDSPGRYEIMNFKEMG
KDYFDYINVGSWDNGELKMDDDEVWSKKSNIIRSVCSEPCEKGQIKVIRKGEVSCCWTCT
PCKENEYVFDEYTCKACQLGSWPTDDLTGCDLIPVQYLRWGDPEPIAAVVFACLGLLATL
FVTVVFIIYRDTPVVKSSSRELCYIILAGICLGYLCTFCLIAKPKQIYCYLQRIGIGLSP
AMSYSALVTKTNRIARILAGSKKKICTKKPRFMSACAQLVIAFILICIQLGIIVALFIME
PPDIMHDYPSIREVYLICNTTNLGVVTPLGYNGLLILSCTFYAFKTRNVPANFNEAKYIA
FTMYTTCIIWLAFVPIYFGSNYKIITMCFSVSLSATVALGCMFVPKVYIILAKPERNVRS
AFTTSTVVRMHVGDGKSSSAASRSSSLVNLWKRRGSSGETL

Ligands and cofactors

ID	Name	Formula	Copies
YKU	3-cyano-N-(1,3-diphenyl-1H-pyrazol-5-yl)benzamide	C23 H16 N4 O	2

Primary citation

Stepwise activation of a metabotropic glutamate receptor. Krishna Kumar, K., Wang, H., Habrian, C. et al. Nature (2024) 629:951-956. DOI 10.1038/s41586-024-07327-x · PubMed

Other PDB entries of the same protein (UniProt P41594 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6FFI 2.2 Å, Crystal Structure of mGluR5 in complex with MMPEP at 2.2 A
9HC0 2.33 Å, Dark structure of the human metabotropic glutamate receptor 5 transmembrane domain bound…
3LMK 2.44 Å, Ligand Binding Domain of Metabotropoc glutamate receptor mGluR5 complexed with glutamate
7P2L 2.54 Å, thermostabilised 7TM domain of human mGlu5 receptor bound to photoswitchable ligand…
4OO9 2.6 Å, Structure of the human class C GPCR metabotropic glutamate receptor 5 transmembrane…
5CGD 2.6 Å, Structure of the human class C GPCR metabotropic glutamate receptor 5 transmembrane…
6FFH 2.65 Å, Crystal Structure of mGluR5 in complex with Fenobam at 2.65 A
8TAO 2.9 Å, Quis and CDPPB bound active mGlu5
9HC3 2.9 Å, Apo-state structure of the human metabotropic glutamate receptor 5 transmembrane domain…
8T8M 3.0 Å, Quis-bound intermediate mGlu5
8X0G 3.0 Å, Human FL Metabotropic glutamate receptor 5, mGlu5-5M with quisqualate, Acc conformation…
8X0B 3.1 Å, Human FL Metabotropic glutamate receptor 5, mGlu5-5M with Quisqualate and VU0424465

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