6E5V: Human mGlu8 receptor amino terminal domain

human mGlu8 receptor amino terminal domain in complex with (S)-3,4-Dicarboxyphenylglycine (DCPG). Determined by X-ray diffraction at 2.95 Å resolution. Released 7 Nov 2018.

Method: X-ray diffraction
Resolution: 2.95 Å
Organism: Homo sapiens
Chains: 2
Atoms: 6,754
Mol. weight: 118.21 kDa
Ligands: HVG
Released: 7 Nov 2018

Explore 6E5V in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6E5V contains 35 α-helices and 40 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: 16 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	40-42	3	1
β-strand	46-52	7	1
β-strand	55-57	3	2
α-helix	58	1
β-strand	64-67	4	2
α-helix	69-74	6
α-helix	75-88	14
β-strand	98-104	7	1
α-helix	109-116	8
β-strand	147-151	5	1
α-helix	156-166	11
β-strand	173-175	3	1
α-helix	181-184	4
β-strand	192-194	3	1
α-helix	199-212	14
β-strand	217-223	7	3
α-helix	226-241	16
β-strand	246-253	8	3
α-helix	261-269	9
β-strand	277-281	5	3
α-helix	284-296	13
β-strand	304-307	4	3
β-strand	329-333	5	3
α-helix	339-346	8
α-helix	359-367	9
α-helix	402-423	22
α-helix	432-434	3
α-helix	439-448	10
β-strand	451-453	3	4
β-strand	457-459	3	4
β-strand	470-478	9	3
β-strand	483-492	10	3
β-strand	494-497	4	3
α-helix	499-501	3

Chain B: 19 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	39-42	4	5
β-strand	46-52	7	5
β-strand	55-57	3	6
α-helix	58-59	2
β-strand	64-67	4	6
α-helix	69-74	6
α-helix	75-88	14
α-helix	97	1
β-strand	98-104	7	5
α-helix	109-120	12
α-helix	145-146	2
β-strand	147-151	5	5
α-helix	156-166	11
β-strand	173-175	3	5
α-helix	181-184	4
β-strand	192-194	3	5
α-helix	197-198	2
α-helix	199-213	15
β-strand	217-223	7	7
α-helix	226-239	14
β-strand	246-253	8	7
α-helix	261-269	9
β-strand	277-281	5	7
α-helix	284-296	13
β-strand	304-307	4	7
β-strand	329-333	5	7
α-helix	339-346	8
α-helix	359-366	8
β-strand	370	1	8
β-strand	383	1	8
β-strand	390	1	9
β-strand	394	1	9
α-helix	402-423	22
α-helix	432-434	3
α-helix	439-447	9
β-strand	450-452	3	10
β-strand	458-460	3	10
β-strand	471-478	8	7
β-strand	483-492	10	7
β-strand	494-497	4	7
α-helix	499-501	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Metabotropic glutamate receptor 8	A, B	protein	523	Homo sapiens	O00222 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6E5V_1 Metabotropic glutamate receptor 8 (chains A, B)
MALVCEGKRSASCPCFFLLTAKFYWILTMMRTHSQEYAHSIRVDGDIILGGLFPVHAKGE
RGVPCGELKKEKGIHRLEAMLYAIDQINKDPDLLSNITLGVRILDTCSRDTYALEQSLTF
VQALIEKDASDVKCANGDPPIFTKPDKISGVIGAAASSVSIMVANILRLFKIPQISYAST
APELSDNTRYDFFSRVVPPDSYQAQAMVDIVTALGWNYVSTLASEGNYGESGVEAFTQIS
REIGGVSIAQSQKIPREPRPGEFEKIIKRLLETPNARAVIMFANEDDIRRILEAAKKLNQ
SGHFLWIGSDSWGSKIAPVYQQEEIAEGAVTILPKRASIDGFDRYFRSRTLANNRRNVWF
AEFWEENFGCKLGSHGKRNSHIKKCTGLERIARDSSYEQEGKVQFVIDAVYSMAYALHNM
HKDLCPGYIGLCPRMSTIDGKELLGYIRAVNFNGSAGTPVTFNENGDAPGRYDIFQYQIT
NKSTEYKVIGHWTNQLHLKVEDMQWAHRENLYFQGEGHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
HVG	4-[(S)-amino(carboxy)methyl]benzene-1,2-dicarboxylic acid	C10 H9 N O6	2

Water and common crystallization additives (CL) are not listed.

Primary citation

Structural Basis for ( S)-3,4-Dicarboxyphenylglycine (DCPG) As a Potent and Subtype Selective Agonist of the mGlu8Receptor. Chen, Q., Ho, J.D., Ashok, S. et al. J Med Chem (2018) 61:10040-10052. DOI 10.1021/acs.jmedchem.8b01120 · PubMed

Other PDB entries of the same protein (UniProt O00222 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6BSZ 2.65 Å, Human mGlu8 Receptor complexed with glutamate
9N8Y 2.76 Å, Cryo EM Structure of Full Length mGluR8 Bound to Agonist L-AP4 and PAM VU6005649
6BT5 2.92 Å, Human mGlu8 Receptor complexed with L-AP4
9MB9 2.97 Å, Cryo-EM structure of Gi-bound GPCR
9MBC 2.97 Å, Cryo-EM structure of agonist-bound GPCR
9N8Z 2.97 Å, Cryo EM Structure of Full Length mGluR8 Bound to Agonist L-AP4 and PAM VU6005649, class 2
9MBA 3.14 Å, Cryo-EM structure of complex of transducer-bound GPCR
9MBB 3.25 Å, Cryo-EM structure of antagonist-bound GPCR
9MBD 3.32 Å, Cryo-EM structure of Apo-GPCR
9Y1M 3.32 Å, Cryo EM Structure of Full Length mGluR8 in Complex with Beta-Arrestin-1 Bound to Agonist…
9Y1N 6.18 Å, Cryo EM Structure of Full lengthmGluR8 Bound to Agonist L-AP4 and PAM VU6005649 in…

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