8YKV: Succinate receptor SUCR1

Cryo-EM structure of succinate receptor SUCR1 bound to compound 31. Determined by electron microscopy at 2.48 Å resolution. Released 29 May 2024.

Method: Electron microscopy
Resolution: 2.48 Å
Organisms: Homo sapiens, Rattus norvegicus, synthetic construct
Chains: 5
Atoms: 8,665
Mol. weight: 151.13 kDa
Ligands: A1LYV
Released: 29 May 2024

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

Secondary structure: helices and β-sheets

8YKV contains 43 α-helices and 58 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 A: 11 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	7-31	25
β-strand	34-40	7	1
α-helix	46-52	7
β-strand	185-191	7	1
β-strand	194-200	7	1
α-helix	208-210	3
α-helix	212-215	4
β-strand	220-226	7	1
α-helix	227-231	5
α-helix	242-254	13
α-helix	257-259	3
β-strand	263-269	7	1
α-helix	271-278	8
α-helix	283-285	3
α-helix	296-309	14
β-strand	319-323	5	1
α-helix	330-350	21

Chain B: 4 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	5-25	21
α-helix	30-33	4
α-helix	34-36	3
α-helix	38-42	5
β-strand	47-51	5	2
β-strand	58-63	6	3
β-strand	69-74	6	3
β-strand	78-83	6	3
β-strand	88-94	7	3
β-strand	100-105	6	4
β-strand	111-116	6	4
β-strand	121-125	5	4
β-strand	134-139	6	4
β-strand	146-151	6	5
β-strand	156-161	6	5
β-strand	166-170	5	5
β-strand	175-180	6	5
β-strand	187-192	6	6
β-strand	198-203	6	6
β-strand	208-212	5	6
β-strand	218-222	5	6
β-strand	229-234	6	7
β-strand	240-245	6	7
β-strand	250-254	5	7
β-strand	259-264	6	7
β-strand	273-278	6	8
β-strand	284-289	6	8
β-strand	294-298	5	8
β-strand	304-308	5	8
β-strand	317-320	4	2
β-strand	327-330	4	2
β-strand	336-339	4	2

Chain E: 4 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	9
β-strand	10-12	3	10
β-strand	17-25	9	9
α-helix	29-31	3
β-strand	33-39	7	10
β-strand	45-51	7	10
β-strand	58-60	3	10
β-strand	69-73	5	9
β-strand	78-84	7	9
α-helix	88-90	3
β-strand	92-99	8	10
β-strand	110-111	2	10
β-strand	115-119	5	10
α-helix	137-139	3
β-strand	140-141	2	11
β-strand	146-148	3	12
β-strand	155-161	7	11
β-strand	166	1	13
β-strand	172	1	13
β-strand	174-179	6	12
β-strand	185-190	6	12
β-strand	194-195	2	12
α-helix	196	1
β-strand	203-207	5	11
β-strand	211-216	6	11
β-strand	225-231	7	12
β-strand	238-239	2	12
β-strand	243-246	4	12

Chain G: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	8-23	16
α-helix	30-43	14
α-helix	45-47	3
α-helix	53-55	3
α-helix	56-58	3

Chain R: 19 helices, 0 β-strands

Element	Residues	Length
α-helix	12-20	9
α-helix	21-25	5
α-helix	26-44	19
α-helix	57-73	17
α-helix	76-85	10
α-helix	92-125	34
α-helix	132-134	3
α-helix	136-154	19
α-helix	155-157	3
α-helix	175-177	3
α-helix	181-192	12
α-helix	193-197	5
α-helix	198-216	19
α-helix	225-226	2
α-helix	228-259	32
α-helix	269-284	16
α-helix	287-292	6
α-helix	293-297	5
α-helix	300-308	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Guanine nucleotide-binding protein G(i) subunit alpha-1	A	protein	354	Homo sapiens	P63096 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	340	Rattus norvegicus	P54311 (AlphaFold model)
Antibody fragment ScFv16	E	protein	247	synthetic construct
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	G	protein	71	Bos taurus	P63212 (AlphaFold model)
Succinate receptor 1	R	protein	334	Homo sapiens	Q9BXA5 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8YKV_1 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains A)
MGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKNTIVKQMKIIHEAG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TTGIVETHFTFKDLHFKMFDVGAQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEM
NRMHASMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAA
AYIQCQFEDLNKRKDTKEIYTHFTCSTDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 2 (B), FASTA

>8YKV_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
MSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLAKIYA
MHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGGLDNI
CSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQTTTF
TGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFPNGNA
FATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNVWDAL
KADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 3 (E), FASTA

>8YKV_3 Antibody fragment ScFv16 (chains E)
VQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYYA
DTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVSS
GGGGSGGGGSGGGGSSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLEL

Sequence of entity 4 (G), FASTA

>8YKV_4 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 5 (R), FASTA

>8YKV_5 Succinate receptor 1 (chains R)
MLGIMAWNATCKNWLAAEAALEKYYLSIFYGIEFVVGVLGNTIVVYGYIFSLKNWNSSNI
YLFNLSVSDLAFLCTLPMLIRSYANGNWIYGDVLCISNRYVLHANLYTSILFLTFISIDR
YLIIKYPFREHLLQKKEFAILISLAIWVLVTLELLPILPLINPVITDNGTTCNDFASSGD
PNYNLIYSMCLTLLGFLIPLFVMCFFYYKIALFLKQRNRQVATALPLEKPLNLVIMAVVI
FSVLFTPYHVMRNVRIASRLGSWKQYQCTQVVINSFYIVTRPLAFLNSVINPVFYFLLGD
HFRDMLMNQLRHNFKSLTSFSRWAHELLLSFREK

Ligands and cofactors

ID	Name	Formula	Copies
A1LYV	(2~{S})-2-[[6-[4-(trifluoromethyloxy)phenyl]pyridin-2-yl]carbonylamino]butanedi…	C17 H13 F3 N2 O6	1

Primary citation

Molecular basis of ligand recognition and activation of the human succinate receptor SUCR1. Li, C., Liu, H., Li, J. et al. Cell Res (2024) 34:594-596. DOI 10.1038/s41422-024-00984-7 · PubMed

Other PDB entries of the same protein (UniProt P63096 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6CRK 2.0 Å, Heterotrimeric G-protein in complex with an antibody fragment
3UMR 2.04 Å, Crystal structure of the G202D mutant of human G-alpha-i1
9P7Z 2.1 Å, NTSR1-Gi-NTS(8-13) Complex in the Canonical, AHD Open State (C-Open-Apo)
2OM2 2.2 Å, Crystal Structure Of Human G[alpha]i1 Bound To The Goloco Motif Of Rgs14
8YN9 2.3 Å, Cryo-EM structure of histamine H4 receptor in complex with histamine and Gi
9HYI 2.3 Å, DP81-bound serotonin 5-HT1A receptor - Gi Protein Complex
9O36 2.3 Å, CryoEM structure of mu-opioid receptor - Gi protein complex bound to fluornitrazene (FNZ)
9P80 2.3 Å, NTSR1-Gi-NTS(8-13) Complex in the Non-Canonical, AHD Open State (NC-Open-Apo)
8XXV 2.33 Å, Cryo-EM Structure of the Prostaglandin D2 Receptor 2-indomethacin Coupled to G Protein
3UMS 2.34 Å, Crystal structure of the G202A mutant of human G-alpha-i1
3ONW 2.38 Å, Structure of a G-alpha-i1 mutant with enhanced affinity for the RGS14 GoLoco motif.
20ZG 2.4 Å, Cryo-EM structure of the human neurotensin receptor 1 (hNTSR1)-Gi1 complex in the…

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