8YIC: SAR247799-bound S1PR1-Gi protein complex

SAR247799-bound S1PR1-Gi protein complex. Determined by electron microscopy at 3.47 Å resolution. Released 11 Dec 2024.

Method: Electron microscopy
Resolution: 3.47 Å
Organisms: Homo sapiens, Enterobacteria phage T4
Chains: 4
Atoms: 7,307
Mol. weight: 145.92 kDa
Ligands: A1LYQ
Released: 11 Dec 2024

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

Secondary structure: helices and β-sheets

8YIC contains 29 α-helices and 44 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, 7 β-strands

Element	Residues	Length	Sheet
α-helix	7-29	23
β-strand	33-40	8	1
α-helix	46-50	5
β-strand	185-191	7	1
β-strand	194-200	7	1
α-helix	208-210	3
α-helix	212-214	3
β-strand	220-225	6	1
α-helix	233-234	2
α-helix	240-242	3
α-helix	244-254	11
β-strand	263	1	1
β-strand	266-268	3	1
α-helix	272-278	7
α-helix	296-308	13
β-strand	321-323	3	1
α-helix	328-351	24

Chain B: 5 helices, 35 β-strands

Element	Residues	Length	Sheet
α-helix	2-24	23
α-helix	30-33	4
α-helix	38-43	6
β-strand	47-49	3	2
β-strand	52	1	3
β-strand	58-61	4	4
β-strand	69	1	5
β-strand	72-74	3	4
β-strand	78-82	5	6
β-strand	83	1	5
β-strand	89-94	6	6
α-helix	95	1
β-strand	100-105	6	7
β-strand	111-116	6	7
β-strand	120	1	8
β-strand	121-125	5	7
β-strand	134-137	4	7
β-strand	140	1	8
α-helix	145	1
β-strand	146-151	6	9
β-strand	157-161	5	9
β-strand	165-168	4	9
β-strand	178-181	4	9
β-strand	187-191	5	10
β-strand	198-203	6	10
β-strand	207-212	6	10
β-strand	218-221	4	10
β-strand	232-234	3	11
β-strand	240-243	4	11
β-strand	250-254	5	11
β-strand	262-264	3	11
β-strand	276-277	2	12
β-strand	284-285	2	13
β-strand	286-287	2	12
β-strand	295-298	4	13
β-strand	303-307	5	13
β-strand	315-320	6	2
β-strand	327-331	5	2
β-strand	335	1	3
β-strand	336-339	4	2

Chain C: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	7-22	16
α-helix	30-43	14
α-helix	56-58	3

Chain R: 11 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	22-32	11
α-helix	47-72	26
α-helix	79-103	25
α-helix	114-147	34
α-helix	157-176	20
α-helix	177-179	3
β-strand	191	1	14
β-strand	199	1	14
α-helix	200-235	36
α-helix	249-281	33
α-helix	293-305	13
α-helix	308-313	6
α-helix	316-324	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Guanine nucleotide-binding protein G(i) subunit alpha-1	A	protein	364	Homo sapiens	P63096 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	343	Homo sapiens	P62873 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	C	protein	71	Homo sapiens	P59768 (AlphaFold model)
Endolysin,Sphingosine 1-phosphate receptor 1	R	protein	515	Enterobacteria phage T4, Homo sapiens	P00720, P21453

Sequence of entity 1 (A), FASTA

>8YIC_1 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains A)
EQKLISEEDLMGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKSTIV
KQMKIIHEAGYSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVL
AGAAEEGFMTAELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPT
QQDVLRTRVKTTGIVETHFTFKDLHFKMFDVGGQRSERKKWIHCFEGVTAIIFCVALSDY
DLVLAEDEEMNRMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEY
AGSNTYEEAAAYIQCQFEDLNKRKDTKEIYTHFTCATDTKNVQFVFDAVTDVIIKNNLKD
CGLF

Sequence of entity 2 (B), FASTA

>8YIC_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
GSSGSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLAK
IYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGGL
DNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQT
TTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFPN
GNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNVW
DALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 3 (C), FASTA

>8YIC_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains C)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 4 (R), FASTA

>8YIC_4 Endolysin,Sphingosine 1-phosphate receptor 1 (chains R)
DYKDDDDANIFEMLRIDEGLRLKIYKNTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRN
TNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAG
FTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYMGPTSVPLVKAH
RSSVSDYVNYDIIVRHYNYTGKLNISADKENSIKLTSVVFILICCFIILENIFVLLTIWK
TKKFHRPMYYFIGNLALSDLLAGVAYTANLLLSGATTYKLTPAQWFLREGSMFVALSASV
FSLLAIAIERYITMLKMKLHNGSNNFRLFLLISACWVISLILGGLPIMGWNCISALSSCS
TVLPLYHKHYILFCTTVFTLLLLSIVILYCRIYSLVRTRSRRLTFRKNISKASRSSEKSL
ALLKTVIIVLSVFIACWAPLFILLLLDVGCKVKTCDILFRAEYFLVLAVLNSGTNPIIYT
LTNKEMRRAFIRIMSCCKCPSGDSAHHHHHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
A1LYQ	SAR247799	C21 H16 Cl N3 O5	1

Primary citation

SAR247799-bound S1PR1 in complex with Gi heterotrimer. Xu, Z., Yu, J.J., Wang, K.X. et al. To be published.

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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