8YYW: OXGR1

Cryo-EM structure of OXGR1 bound to alpha-ketoglutarate and Gq proteins. Determined by electron microscopy at 3.16 Å resolution. Released 9 Apr 2025.

Method: Electron microscopy
Resolution: 3.16 Å
Organisms: Vicugna pacos, Homo sapiens
Chains: 5
Atoms: 9,068
Mol. weight: 149.04 kDa
Ligands: AKG
Released: 9 Apr 2025

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

Secondary structure: helices and β-sheets

8YYW contains 34 α-helices and 64 β-strands across 5 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 B: 3 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	10-12	3	2
β-strand	17-25	9	1
α-helix	29-31	3
β-strand	33-39	7	2
β-strand	45-51	7	2
α-helix	53-55	3
β-strand	58-60	3	2
β-strand	68-73	6	1
β-strand	78-84	7	1
α-helix	88-90	3
β-strand	92-99	8	2
β-strand	111-119	9	2
β-strand	140-141	2	3
β-strand	146-148	3	4
β-strand	155-161	7	3
β-strand	166	1	5
β-strand	172	1	5
β-strand	174-179	6	4
β-strand	186-190	5	4
β-strand	194-195	2	4
β-strand	203-207	5	3
β-strand	211-216	6	3
β-strand	226-231	6	4
β-strand	239	1	4
β-strand	243-246	4	4

Chain C: 3 helices, 33 β-strands

Element	Residues	Length	Sheet
α-helix	3-24	22
α-helix	30-33	4
α-helix	38-39	2
β-strand	47-51	5	6
β-strand	58-63	6	7
β-strand	69-74	6	7
β-strand	78-83	6	7
β-strand	88-94	7	7
β-strand	100	1	8
β-strand	104-105	2	9
β-strand	111-115	5	9
β-strand	116	1	8
β-strand	120-125	6	9
β-strand	134-140	7	9
β-strand	146-148	3	10
β-strand	151	1	10
β-strand	156-161	6	10
β-strand	165-170	6	10
β-strand	175-181	7	10
β-strand	187	1	11
β-strand	191-192	2	12
β-strand	198-202	5	12
β-strand	203	1	11
β-strand	207-212	6	12
β-strand	217-223	7	12
β-strand	229-234	6	13
β-strand	240-245	6	13
β-strand	250-254	5	13
β-strand	259-264	6	13
β-strand	273-278	6	14
β-strand	284-289	6	14
β-strand	294-298	5	14
β-strand	304-308	5	14
β-strand	315-320	6	6
β-strand	327-331	5	6
β-strand	336-339	4	6

Chain D: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	8-11	4
α-helix	14-22	9
α-helix	30-43	14
α-helix	45-47	3
α-helix	53-55	3

Chain E: 15 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	29-34	6
α-helix	36-60	25
α-helix	69-84	16
α-helix	86-94	9
α-helix	103-136	34
α-helix	147-170	24
β-strand	174-175	2	15
α-helix	177-179	3
β-strand	182-183	2	15
α-helix	186-188	3
α-helix	192-203	12
α-helix	204-208	5
α-helix	209-224	16
α-helix	238-269	32
α-helix	274-287	14
α-helix	290-302	13
α-helix	307-321	15

Chain F: 8 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	7-30	24
β-strand	34-39	6	16
α-helix	48-51	4
β-strand	185-189	5	16
β-strand	196-200	5	16
α-helix	208-210	3
α-helix	212-215	4
β-strand	220-226	7	16
α-helix	242-254	13
β-strand	263-269	7	16
α-helix	271-280	10
α-helix	296-308	13
β-strand	319-323	5	16
α-helix	330-346	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
ScFv16	B	protein	247	Vicugna pacos
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	C	protein	339	Homo sapiens	P62873 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	D	protein	57	Homo sapiens	P59768 (AlphaFold model)
2-oxoglutarate receptor 1	E	protein	337	Homo sapiens	Q96P68 (AlphaFold model)
Guanine nucleotide-binding protein G(i) subunit alpha-1,Guanine nucleotide-binding protein G(q)…	F	protein	354	Homo sapiens	P50148 (AlphaFold model), P63096

Sequence of entity 1 (B), FASTA

>8YYW_1 ScFv16 (chains B)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLEL

Sequence of entity 2 (C), FASTA

>8YYW_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains C)
SELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLAKIYAM
HWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGGLDNIC
SIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQTTTFT
GHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFPNGNAF
ATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNVWDALK
ADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 3 (D), FASTA

>8YYW_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains D)
ASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENPFRE

Sequence of entity 4 (E), FASTA

>8YYW_4 2-oxoglutarate receptor 1 (chains E)
MNEPLDYLANASDFPDYAAAFGNCTDENIPLKMHYLPVIYGIIFLVGFPGNAVVISTYIF
KMRPWKSSTIIMLNLACTDLLYLTSLPFLIHYYASGENWIFGDFMCKFIRFSFHFNLYSS
ILFLTCFSIFRYCVIIHPMSCFSIHKTRCAVVACAVVWIISLVAVIPMTFLITSTNRTNR
SACLDLTSSDELNTIKWYNLILTATTFCLPLVIVTLCYTTIIHTLTHGLQTDSCLKQKAR
RLTILLLLAFYVCFLPFHILRVIRIESRLLSISCSIENQIHEAYIVSRPLAALNTFGNLL
LYVVVSDNFQQAVCSTVRCKVSGNLEQAKKISYSNNP

Sequence of entity 5 (F), FASTA

>8YYW_5 Guanine nucleotide-binding protein G(i) subunit alpha-1,Guanine nucleotide-binding protein G(q) subunit alpha (chains F)
MGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKSTIVKQMKIIHEAG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TTGIVETHFTFKDLHFKMFDVGAQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEM
NRMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAA
AYIQCQFEDLNKRKDTKEIYTHFTCSTDTENIRFVFAAVKDTILQLNLKEYNLV

Ligands and cofactors

ID	Name	Formula	Copies
AKG	2-oxoglutaric acid	C5 H6 O5	2

Primary citation

Molecular insights into ligand recognition and signaling of OXGR1. Liu, A., Liu, Y., Long, Y. et al. Nat Commun (2025) 16:11205-11205. DOI 10.1038/s41467-025-67101-z · PubMed

Other PDB entries of the same protein (UniProt P62873 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8QEH 1.43 Å, Crystal structure of the G11 protein heterotrimer bound to FR900359 inhibitor
8QEG 1.7 Å, Crystal structure of the G11 protein heterotrimer bound to YM-254890 inhibitor
8F0K 1.9 Å, Human Amylin3 Receptor in complex with Gs and Pramlintide analogue peptide San385
9YDQ 1.94 Å, Human delta opioid receptor complex with mini-Gi and agonist DADLE and allosteric…
9YDP 1.95 Å, Human delta opioid receptor complex with mini-Gi and agonist DADLE
6CRK 2.0 Å, Heterotrimeric G-protein in complex with an antibody fragment
8F0J 2.0 Å, Calcitonin Receptor in complex with Gs and Pramlintide analogue peptide San45
8F2B 2.0 Å, Amylin 3 Receptor in complex with Gs and Pramlintide analogue peptide San45
9XXT 2.0 Å, Cryo-EM structure of lysophosphatidylserine (18:0)-bound GPR174-Gs complex
6X18 2.1 Å, GLP-1 peptide hormone bound to Glucagon-Like peptide-1 (GLP-1) Receptor
6X19 2.1 Å, Non peptide agonist CHU-128, bound to Glucagon-Like peptide-1 (GLP-1) Receptor
9NTU 2.1 Å, Cryo-EM structure of BETP-GLP-1(9-36)-GLP-1R-Gs complex

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