8JPP: Succinate receptor

Cryo-EM structure of succinate receptor bound to succinate acid coupling MiniGsq. Determined by electron microscopy at 3.2 Å resolution. Released 22 May 2024.

Method: Electron microscopy
Resolution: 3.2 Å
Organisms: Homo sapiens, Escherichia coli, Oplophorus gracilirostris
Chains: 4
Atoms: 7,137
Mol. weight: 153.27 kDa
Ligands: SIN
Released: 22 May 2024

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

Secondary structure: helices and β-sheets

8JPP contains 33 α-helices and 35 β-strands across 4 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: 9 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	13-39	27
β-strand	41-46	6	1
α-helix	53-61	9
β-strand	208-214	7	1
β-strand	217-223	7	1
α-helix	234-240	7
β-strand	243-249	7	1
α-helix	259-267	9
β-strand	276-282	7	1
α-helix	284-292	9
α-helix	298-301	4
α-helix	303-305	3
α-helix	322-340	19
β-strand	349-353	5	1
α-helix	361-380	20

Chain B: 4 helices, 29 β-strands

Element	Residues	Length	Sheet
α-helix	11-25	15
α-helix	30-33	4
α-helix	34-36	3
β-strand	47-50	4	2
β-strand	58-63	6	3
β-strand	69-74	6	3
β-strand	78-83	6	3
β-strand	89-94	6	3
α-helix	95	1
β-strand	103-105	3	4
β-strand	111-114	4	4
β-strand	116	1	5
β-strand	120-125	6	4
β-strand	134-140	7	4
β-strand	146-153	8	5
β-strand	156-161	6	5
β-strand	165-168	4	5
β-strand	178-181	4	5
β-strand	187-192	6	6
β-strand	198-203	6	6
β-strand	208-212	5	6
β-strand	217-222	6	6
β-strand	229-232	4	7
β-strand	240-245	6	7
β-strand	250-254	5	7
β-strand	260-264	5	7
β-strand	273-278	6	8
β-strand	284-289	6	8
β-strand	294-298	5	8
β-strand	304-307	4	8
β-strand	315-320	6	2
β-strand	327-331	5	2
β-strand	337-339	3	2

Chain G: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	15-23	9
α-helix	30-43	14
α-helix	54-55	2

Chain R: 17 helices, 0 β-strands

Element	Residues	Length
α-helix	11-20	10
α-helix	21-25	5
α-helix	26-49	24
α-helix	57-74	18
α-helix	76-85	10
α-helix	91-125	35
α-helix	136-153	18
α-helix	155-157	3
α-helix	158-161	4
α-helix	181-192	12
α-helix	193-197	5
α-helix	198-220	23
α-helix	228-257	30
α-helix	267-284	18
α-helix	287-291	5
α-helix	292-297	6
α-helix	302-316	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Guanine nucleotide-binding protein G(s) subunit alpha isoforms short	A	protein	253	Homo sapiens	P63092 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	377	Homo sapiens	P62873 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	G	protein	71	Homo sapiens	P59768 (AlphaFold model)
Soluble cytochrome b562,Succinate receptor 1,Oplophorus-luciferin 2-monooxygenase catalytic subunit	R	protein	658	Escherichia coli, Homo sapiens, Oplophorus gracilirostris	P0ABE7 (AlphaFold model), Q9BXA5

Sequence of entity 1 (A), FASTA

>8JPP_1 Guanine nucleotide-binding protein G(s) subunit alpha isoforms short (chains A)
MGCLGNSKTEDQRNEEKAQREANKKIEKQLQKDKQVYRATHRLLLLGADNSGKSTIVKQM
RILHGGSGGSGGTSGIFETKFQVDKVNFHMFDVGGQRDERRKWIQCFNDVTAIIFVVDSS
DYNRLQEALNLFKSIWNNRWLRTISVILFLNKQDLLAEKVLAGKSKIEDYFPEFARYTTP
EDATPEPGEDPRVTRAKYFIRDEFLRISTASGDGRHYCYPHFTCAVDTENARRIFNDCKD
IILQMNLREYNLV

Sequence of entity 2 (B), FASTA

>8JPP_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
MHHHHHHGSLLQSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRR
TLRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSG
NYVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALW
DIETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDI
NAICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGY
DDFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWNGSSGGGGSG
GGGSSGVSGWRLFKKIS

Sequence of entity 3 (G), FASTA

>8JPP_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 4 (R), FASTA

>8JPP_4 Soluble cytochrome b562,Succinate receptor 1,Oplophorus-luciferin 2-monooxygenase catalytic subunit (chains R)
MKTIIALSYIFCLVFADYKDDDDAGRAHHHHHHHHHHENLYFQSGAPADLEDNWETLNDN
LKVIEKADNAAQVKDALTKMRAAALDAQKATPPKLEDKSPDSPEMKDFRHGFDILVGQID
DALKLANEGKVKEAQAAAEQLKTTRNAYIQKYLLEVLFQGPEFMLGIMAWNATCKNWLAA
EAALEKYYLSIFYGIEFVVGVLGNTIVVYGYIFSLKNWNSSNIYLFNLSVSDLAFLCTLP
MLIRSYANGNWIYGDVLCISNRYVLHANLYTSILFLTFISIDRYLIIKYPFREHLLQKKE
FAILISLAIWVLVTLELLPILPLINPVITDNGTTCNDFASSGDPNYNLIYSMCLTLLGFL
IPLFVMCFFYYKIALFLKQRNRQVATALPLEKPLNLVIMAVVIFSVLFTPYHVMRNVRIA
SRLGSWKQYQCTQVVINSFYIVTRPLAFLNSVINPVFYFLLGDHFRDMLMNQLRHNFKSL
TSFSRWAHELLLSFREKAAAVFTLEDFVGDWEQTAAYNLDQVLEQGGVSSLLQNLAVSVT
PIQRIVRSGENALKIDIHVIIPYEGLSADQMAQIEEVFKVVYPVDDHHFKVILPYGTLVI
DGVTPNMLNYFGRPYEGIAVFDGKKITVTGTLWNGNKIIDERLITPDGSMLFRVTINS

Ligands and cofactors

ID	Name	Formula	Copies
SIN	Succinic acid	C4 H6 O4	1

Primary citation

Molecular activation and G protein coupling selectivity of human succinate receptor SUCR1. Wang, T., Tang, W., Zhu, X. et al. Cell Res (2024) 34:590-593. DOI 10.1038/s41422-024-00968-7 · PubMed

Other PDB entries of the same protein (UniProt P63092 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7BPH 1.57 Å, Crystal structure of GppNHp-bound GNAS in complex with the cyclic peptide inhibitor GN13
6AU6 1.7 Å, Crystal structure of GDP-bound human GNAS R201C mutant
8F0K 1.9 Å, Human Amylin3 Receptor in complex with Gs and Pramlintide analogue peptide San385
7E5E 1.95 Å, Crystal structure of GDP-bound GNAS in complex with the cyclic peptide inhibitor GD20
7MBX 1.95 Å, Human Cholecystokinin 1 receptor (CCK1R) Gs complex
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
7RTB 2.14 Å, Peptide-19 bound to the Glucagon-Like Peptide-1 Receptor (GLP-1R)

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