6N4Y: Metabotropic glutamate receptor 5

Metabotropic Glutamate Receptor 5 Extracellular Domain with Nb43. Determined by X-ray diffraction at 3.26 Å resolution. Released 23 Jan 2019.

Method: X-ray diffraction
Resolution: 3.26 Å
Organisms: Homo sapiens, Lama glama
Chains: 8
Atoms: 19,626
Mol. weight: 327.6 kDa
Ligands: NAG
Released: 23 Jan 2019

Explore 6N4Y in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6N4Y contains 100 α-helices and 140 β-strands across 8 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: 23 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	29-31	3	1
β-strand	35-41	7	1
β-strand	44	1	2
α-helix	45-48	4
β-strand	60	1	2
α-helix	62-66	5
α-helix	67-81	15
β-strand	91-97	7	1
α-helix	102-118	17
β-strand	143-147	5	1
α-helix	152-162	11
β-strand	169-171	3	1
α-helix	177-180	4
β-strand	188-190	3	1
α-helix	195-208	14
β-strand	213-219	7	3
α-helix	222-237	16
β-strand	241-248	8	3
α-helix	254-266	13
β-strand	273-277	5	3
α-helix	280-293	14
β-strand	300-303	4	3
α-helix	305-307	3
α-helix	311-314	4
α-helix	318-321	4
β-strand	325-329	5	3
α-helix	332-334	3
α-helix	335-342	8
α-helix	355-362	8
β-strand	366	1	4
β-strand	380	1	4
α-helix	381-382	2
α-helix	397-418	22
α-helix	427-429	3
α-helix	434-442	9
β-strand	445-447	3	5
α-helix	452	1
β-strand	453-455	3	5
α-helix	461-463	3
β-strand	465-473	9	3
β-strand	479-488	10	3
β-strand	491-494	4	3
α-helix	513-515	3
β-strand	522-524	3	6
β-strand	532-534	3	6

Chain B: 24 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	25-27	3
β-strand	29-31	3	7
β-strand	35-41	7	7
β-strand	44	1	8
α-helix	45-48	4
β-strand	60	1	8
α-helix	62-67	6
α-helix	68-81	14
β-strand	91-97	7	7
α-helix	102-112	11
α-helix	115-117	3
α-helix	141-142	2
β-strand	143-147	5	7
α-helix	152-162	11
β-strand	169-171	3	7
α-helix	177-180	4
β-strand	188-190	3	7
α-helix	195-207	13
β-strand	213-219	7	9
α-helix	222-237	16
β-strand	241-248	8	9
α-helix	254-266	13
β-strand	273-277	5	9
α-helix	280-293	14
β-strand	300-303	4	9
α-helix	305-307	3
α-helix	311-314	4
α-helix	318-321	4
β-strand	325-329	5	9
α-helix	332-334	3
α-helix	335-341	7
α-helix	355-362	8
β-strand	365-366	2	10
β-strand	379-380	2	10
α-helix	397-418	22
α-helix	427-429	3
α-helix	434-441	8
β-strand	445-447	3	11
α-helix	452	1
β-strand	453-455	3	11
β-strand	465-475	11	9
β-strand	478-488	11	9
β-strand	491-493	3	9
β-strand	521-523	3	12
β-strand	533-535	3	12
α-helix	536-538	3
β-strand	541-543	3	13
β-strand	549-551	3	13

Chain C: 22 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	29-31	3	14
β-strand	35-41	7	14
β-strand	44	1	15
α-helix	45-48	4
β-strand	60	1	15
α-helix	62-66	5
α-helix	67-81	15
β-strand	91-97	7	14
α-helix	102-113	12
α-helix	115-117	3
β-strand	143-147	5	14
α-helix	152-162	11
β-strand	169-171	3	14
α-helix	177-180	4
β-strand	188-190	3	14
α-helix	193-194	2
α-helix	195-208	14
β-strand	213-219	7	16
α-helix	222-237	16
β-strand	241-248	8	16
α-helix	253-267	15
β-strand	273-277	5	16
α-helix	280-292	13
β-strand	300-303	4	16
α-helix	305-307	3
α-helix	311-314	4
α-helix	318-321	4
β-strand	325-329	5	16
α-helix	335-341	7
α-helix	355-362	8
β-strand	365-366	2	17
β-strand	379-380	2	17
α-helix	381-382	2
α-helix	397-418	22
α-helix	427-429	3
α-helix	434-442	9
β-strand	445-447	3	18
β-strand	453-455	3	18
α-helix	461-463	3
β-strand	465-475	11	16
β-strand	478-488	11	16
β-strand	491-494	4	16
β-strand	521-523	3	19
β-strand	533-535	3	19

Chain D: 22 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	29-31	3	20
β-strand	35-41	7	20
β-strand	44	1	21
α-helix	45-48	4
β-strand	60	1	21
α-helix	62-67	6
α-helix	68-81	14
β-strand	91-97	7	20
α-helix	102-113	12
α-helix	115-117	3
α-helix	141-142	2
β-strand	143-147	5	20
α-helix	152-162	11
α-helix	163-165	3
β-strand	169-171	3	20
α-helix	177-180	4
β-strand	188-190	3	20
α-helix	195-208	14
β-strand	213-219	7	22
α-helix	222-237	16
β-strand	241-248	8	22
α-helix	254-265	12
β-strand	273-277	5	22
α-helix	280-293	14
β-strand	300-303	4	22
α-helix	305-307	3
α-helix	311-313	3
α-helix	318-321	4
β-strand	325-329	5	22
α-helix	335-342	8
α-helix	355-362	8
β-strand	366	1	23
β-strand	380	1	23
α-helix	397-418	22
α-helix	427-429	3
α-helix	434-442	9
β-strand	445-447	3	24
α-helix	452	1
β-strand	453-455	3	24
β-strand	465-473	9	22
β-strand	479-488	10	22
β-strand	491-494	4	22
β-strand	521-523	3	25
β-strand	533-535	3	25
β-strand	541-545	5	26
β-strand	548-551	4	26

Chain E: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	6-9	4	27
β-strand	12-15	4	28
β-strand	19-26	8	27
α-helix	31-33	3
β-strand	35-41	7	28
β-strand	48-53	6	28
β-strand	60-62	3	28
β-strand	70-75	6	27
β-strand	80-86	7	27
α-helix	90-92	3
β-strand	94-101	8	28
β-strand	114-115	2	28
β-strand	119-124	6	28

Chain F: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	5-9	5	29
β-strand	12-15	4	30
β-strand	20-27	8	29
α-helix	31-33	3
β-strand	35-41	7	30
β-strand	48-53	6	30
β-strand	60-62	3	30
β-strand	70-75	6	29
β-strand	80-85	6	29
α-helix	90-92	3
β-strand	94-104	11	30
β-strand	110-115	6	30
β-strand	116	1	29
β-strand	119-124	6	30

Chain G: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	6-9	4	31
β-strand	12-14	3	32
β-strand	20-26	7	31
α-helix	31-33	3
β-strand	35-41	7	32
β-strand	48-53	6	32
β-strand	60-62	3	32
β-strand	70-75	6	31
β-strand	80-85	6	31
α-helix	90-92	3
β-strand	94-104	11	32
β-strand	110-114	5	32
β-strand	116	1	31
β-strand	119-123	5	32

Chain H: 3 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	6-9	4	33
β-strand	12-14	3	34
β-strand	20-26	7	33
α-helix	31-33	3
β-strand	35-41	7	35
β-strand	48-53	6	35
β-strand	60-62	3	35
α-helix	64-66	3
β-strand	70-75	6	33
α-helix	76-78	3
β-strand	80-85	6	33
β-strand	95-101	7	35
β-strand	114-115	2	35
β-strand	116	1	33
β-strand	119-120	2	35
β-strand	121-123	3	34

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Metabotropic glutamate receptor 5	A, B, C, D	protein	596	Homo sapiens	P41594 (AlphaFold model)
Nanobody 43	E, F, G, H	protein	123	Lama glama

Sequence of entity 1 (A, B, C, D), FASTA

>6N4Y_1 Metabotropic glutamate receptor 5 (chains A, B, C, D)
MLLVNQSHQGFNKEHTSKMVSAIVLYVLLAAAAHSAFQSSERRVVAHMPGDIIIGALFSV
HHQPTVDKVHERKCGAVREQYGIQRVEAMLHTLERINSDPTLLPNITLGCEIRDSCWHSA
VALEQSIEFIRDSLISSEEEEGLVRCVDGSSSSFRSKKPIVGVIGPGSSSVAIQVQNLLQ
LFNIPQIAYSATSMDLSDKTLFKYFMRVVPSDAQQARAMVDIVKRYNWTYVSAVHTEGNY
GESGMEAFKDMSAKEGICIAHSYKIYSNAGEQSFDKLLKKLTSHLPKARVVACFCEGMTV
RGLLMAMRRLGLAGEFLLLGSDGWADRYDVTDGYQREAVGGITIKLQSPDVKWFDDYYLK
LRPETNHRNPWFQEFWQHRFQCRLEGFPQENSKYNKTCNSSLTLKTHHVQDSKMGFVINA
IYSMAYGLHNMQMSLCPGYAGLCDAMKPIDGRKLLESLMKTNFTGVSGDTILFDENGDSP
GRYEIMNFKEMGKDYFDYINVGSWDNGELKMDDDEVWSKKSNIIRSVCSEPCEKGQIKVI
RKGEVSCCWTCTPCKENEYVFDEYTCKACQLGSWPTDDLTGCDLIPVQHHHHHHHH

Sequence of entity 2 (E, F, G, H), FASTA

>6N4Y_2 Nanobody 43 (chains E, F, G, H)
QVQLVESGGGLVQAGGSLRLSCAASGRTFTSYAMGWFRQAPGKERESVAAISSSGGSTHY
ADSVKGRFTISRDNSKNTVYLQMNSLKPEDTAVYYCAAAMYGSRWPDWEYDYWGQGTQVT
VSS

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	4

Primary citation

Structural insights into the activation of metabotropic glutamate receptors. Koehl, A., Hu, H., Feng, D. et al. Nature (2019) 566:79-84. DOI 10.1038/s41586-019-0881-4 · 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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