7TD4: Sphingosine-1-phosphate receptor 1-Gi complex

Sphingosine-1-phosphate receptor 1-Gi complex bound to Siponimod. Determined by electron microscopy at 2.6 Å resolution. Released 9 Feb 2022.

Method: Electron microscopy
Resolution: 2.6 Å
Organisms: Bos taurus, Rattus norvegicus, Homo sapiens
Chains: 4
Atoms: 6,893
Mol. weight: 133.1 kDa
Ligands: J8C, NAG
Released: 9 Feb 2022

Explore 7TD4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7TD4 contains 30 α-helices and 38 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: 10 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	9-30	22
β-strand	33-40	8	8
α-helix	46-53	8
β-strand	185-190	6	8
β-strand	195-200	6	8
α-helix	208-210	3
α-helix	212-215	4
β-strand	220-226	7	8
α-helix	227-231	5
β-strand	233	1	9
β-strand	241	1	9
α-helix	242-254	13
β-strand	263-269	7	8
α-helix	271-277	7
α-helix	283-285	3
α-helix	296-309	14
β-strand	319-323	5	8
α-helix	331-350	20

Chain B: 3 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	11-23	13
α-helix	30-33	4
α-helix	38-39	2
β-strand	47-51	5	1
β-strand	58-63	6	2
β-strand	69-74	6	2
β-strand	78-83	6	2
β-strand	89-94	6	2
β-strand	100-105	6	3
β-strand	111-116	6	3
β-strand	121-125	5	3
β-strand	134-139	6	3
β-strand	146-153	8	4
β-strand	156-161	6	4
β-strand	165-170	6	4
β-strand	175-181	7	4
β-strand	187-192	6	5
β-strand	198-203	6	5
β-strand	207-212	6	5
β-strand	218-223	6	5
β-strand	229-234	6	6
β-strand	240-245	6	6
β-strand	250-254	5	6
β-strand	259-264	6	6
β-strand	273-278	6	7
β-strand	284-289	6	7
β-strand	294-298	5	7
β-strand	303-307	5	7
β-strand	315-320	6	1
β-strand	327-331	5	1
β-strand	336-339	4	1

Chain G: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	14-23	10
α-helix	30-43	14
α-helix	45-47	3
α-helix	53-55	3
α-helix	56-58	3

Chain R: 12 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	22-32	11
α-helix	48-72	25
α-helix	79-103	25
α-helix	106-108	3
α-helix	114-148	35
α-helix	158-176	19
β-strand	191	1	10
β-strand	199	1	10
α-helix	200-233	34
α-helix	249-281	33
α-helix	283	1
α-helix	289-291	3
α-helix	294-313	20
α-helix	318-322	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	340	Bos taurus	P62871 (AlphaFold model)
Guanine nucleotide-binding protein G(i) subunit alpha-1	A	protein	379	Rattus norvegicus	P10824 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	G	protein	71	Bos taurus	P63212 (AlphaFold model)
Sphingosine 1-phosphate receptor 1	R	protein	392	Homo sapiens	P21453 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>7TD4_1 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
MSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLAKIYA
MHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGGLDNI
CSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQTTTF
TGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFPNGNA
FATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNVWDAL
KADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 2 (A), FASTA

>7TD4_2 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains A)
MGSSHHHHHHSSGLEVLFQGPHMASMGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVK
LLLLGAGESGKSTIVKQMKIIHEAGYSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDF
GDSARADDARQLFVLAGAAEEGFMTAELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYY
LNDLDRIAQPNYIPTQQDVLRTRVKTTGIVETHFTFKDLHFKMFDVGAQRSERKKWIHCF
EGVTAIIFCVALSDYDLVLAEDEEMNRMHESMKLFDSICNNKWFTDTSIILFLNKKDLFE
EKIKKSPLTICYPEYAGSNTYEEAAAYIQCQFEDLNKRKDTKEIYTHFTCATDTKNVQFV
FDAVTDVIIKNNLKDCGLF

Sequence of entity 3 (G), FASTA

>7TD4_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFSAIL

Sequence of entity 4 (R), FASTA

>7TD4_4 Sphingosine 1-phosphate receptor 1 (chains R)
DYKDDDDKAAAGPTSVPLVKAHRSSVSDYVNYDIIVRHYNYTGKLNISADKENSIKLTSV
VFILICCFIILENIFVLLTIWKTKKFHRPMYYFIGNLALSDLLAGVAYTANLLLSGATTY
KLTPAQWFLREGSMFVALSASVFSLLAIAIERYITMLKMKLHNGSNNFRLFLLISACWVI
SLILGGLPIMGWNCISALSSCSTVLPLYHKHYILFCTTVFTLLLLSIVILYCRIYSLVRT
RSRRLTFRKNISKASRSSEKSLALLKTVIIVLSVFIACWAPLFILLLLDVGCKVKTCDIL
FRAEYFLVLAVLNSGTNPIIYTLTNKEMRRAFIRIMSCCKCPSGDSAGKFKRPIIAGMEF
SRSKSDNSSHPQKDEGDNPETIMSSGNVNSSS

Ligands and cofactors

ID	Name	Formula	Copies
J8C	1-[[4-[(~{E})-~{N}-[[4-cyclohexyl-3-(trifluoromethyl)phenyl]methoxy]-~{C}-methy…	C29 H35 F3 N2 O3	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1

Primary citation

Differential activation mechanisms of lipid GPCRs by lysophosphatidic acid and sphingosine 1-phosphate. Liu, S., Paknejad, N., Zhu, L. et al. Nat Commun (2022) 13:731-731. DOI 10.1038/s41467-022-28417-2 · PubMed

Other PDB entries of the same protein (UniProt P62871 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5KDO 1.9 Å, Heterotrimeric complex of the 4 alanine insertion variant of the Gi alpha1 subunit and…
1GOT 2.0 Å, Heterotrimeric complex of a gt-alpha/gi-alpha chimera and the gt-beta-gamma subunits
3V5W 2.07 Å, Human G Protein-Coupled Receptor Kinase 2 in Complex with Soluble Gbetagamma Subunits…
1TBG 2.1 Å, Beta-gamma dimer of the heterotrimeric G-protein transducin
1GP2 2.3 Å, G protein heterotrimer GI_ALPHA_1 BETA_1 GAMMA_2 with GDP bound
5WG4 2.31 Å, Human GRK2 in complex with Gbetagamma subunits and CCG257284
6B20 2.34 Å, Crystal structure of a complex between G protein beta gamma dimer and an inhibitory…
1GG2 2.4 Å, G protein heterotrimer mutant GI_ALPHA_1(G203A) BETA_1 GAMMA_2 with GDP bound
2TRC 2.4 Å, Phosducin/transducin beta-gamma complex
4MK0 2.4 Å, Crystal structure of G protein-coupled receptor kinase 2 in complex with a a rationally…
6U7C 2.44 Å, Human GRK2 in complex with Gbetagamma subunits and CCG258747
3PVU 2.48 Å, Bovine GRK2 in complex with Gbetagamma subunits and a selective kinase inhibitor (CMPD101)

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