8G94: CD69-bound S1PR1 coupled to heterotrimeric Gi

Structure of CD69-bound S1PR1 coupled to heterotrimeric Gi. Determined by electron microscopy at 3.15 Å resolution. Released 19 Apr 2023.

Method: Electron microscopy
Resolution: 3.15 Å
Organisms: Homo sapiens, Mus musculus
Chains: 7
Atoms: 9,221
Mol. weight: 201.73 kDa
Released: 19 Apr 2023

Explore 8G94 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8G94 contains 32 α-helices and 62 β-strands across 7 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, 2 β-strands

Element	Residues	Length	Sheet
α-helix	22-32	11
α-helix	47-72	26
α-helix	83-103	21
α-helix	107-111	5
α-helix	114-147	34
α-helix	157-176	20
β-strand	191	1	1
β-strand	199	1	1
α-helix	200-234	35
α-helix	252-280	29
α-helix	293-313	21
α-helix	316-321	6

Chain B: 9 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	7-31	25
β-strand	33-39	7	2
α-helix	46-51	6
β-strand	185-191	7	2
β-strand	194-200	7	2
α-helix	208-210	3
α-helix	212-215	4
β-strand	220-226	7	2
α-helix	227-229	3
β-strand	233	1	3
β-strand	241	1	3
α-helix	242-254	13
β-strand	263-269	7	2
α-helix	271-280	10
α-helix	296-309	14
β-strand	319	1	2
β-strand	322	1	2
α-helix	330-350	21

Chain C: 3 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	5-24	20
α-helix	38-39	2
β-strand	47-51	5	4
β-strand	58-61	4	5
β-strand	69	1	5
β-strand	72-74	3	5
β-strand	78-83	6	5
β-strand	88-94	7	5
α-helix	95	1
β-strand	100-105	6	6
β-strand	111-116	6	6
β-strand	121-125	5	6
β-strand	134-139	6	6
β-strand	146-151	6	7
β-strand	156-161	6	7
β-strand	165-170	6	7
β-strand	175-181	7	7
β-strand	187-192	6	8
β-strand	198-203	6	8
β-strand	207-212	6	8
β-strand	218-223	6	8
β-strand	229-234	6	9
β-strand	240-245	6	9
β-strand	249-254	6	9
β-strand	259-265	7	9
β-strand	273-278	6	10
β-strand	284-289	6	10
β-strand	294-298	5	10
β-strand	315-320	6	4
β-strand	327-331	5	4
β-strand	336-339	4	4

Chain D: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	7-23	17
α-helix	26-29	4
α-helix	30-43	14
α-helix	54-55	2

Chain E: 4 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	11
β-strand	10-12	3	12
β-strand	17-25	9	11
α-helix	29-31	3
β-strand	33-39	7	12
β-strand	45-51	7	12
α-helix	53-55	3
β-strand	58-60	3	12
β-strand	68-73	6	11
β-strand	78-84	7	11
β-strand	92-99	8	12
β-strand	111	1	12
β-strand	115-119	5	12
α-helix	126-127	2
β-strand	128-130	3	13
β-strand	134-136	3	14
β-strand	144-149	6	13
β-strand	154	1	15
β-strand	160	1	15
β-strand	162-167	6	14
β-strand	174-178	5	14
β-strand	182-183	2	14
α-helix	184	1
β-strand	192-196	5	13
β-strand	199-203	5	13
β-strand	213-219	7	14
β-strand	231-234	4	14

Chain F: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	41-63	23

Chain G: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	42-63	22

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Sphingosine 1-phosphate receptor 1	A	protein	355	Homo sapiens	P21453 (AlphaFold model)
Guanine nucleotide-binding protein G(i) subunit alpha-1	B	protein	354	Homo sapiens	P63096 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	C	protein	345	Homo sapiens	P62873 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	D	protein	71	Homo sapiens	P59768 (AlphaFold model)
scFv16	E	protein	259	Mus musculus
Early activation antigen CD69	F, G	protein	211	Homo sapiens	Q07108

Sequence of entity 1 (A), FASTA

>8G94_1 Sphingosine 1-phosphate receptor 1 (chains A)
MGPTSVPLVKAHRSSVSDYVNYDIIVRHYNYTGKLNISADKENSIKLTSVVFILICCFII
LENIFVLLTIWKTKKFHRPMYYFIGNLALSDLLAGVAYTANLLLSGATTYKLTPAQWFLR
EGSMFVALSASVFSLLAIAIERYITMLKMKLHNGSNNFRLFLLISACWVISLILGGLPIM
GWNCISALSSCSTVLPLYHKHYILFCTTVFTLLLLSIVILYCRIYSLVRTRSRRLTFRKN
ISKASRSSEKSLALLKTVIIVLSVFIACWAPLFILLLLDVGCKVKTCDILFRAEYFLVLA
VLNSGTNPIIYTLTNKEMRRAFIRIMSCCKCPSGDSAGKFKRPIIAGDYKDDDDK

Sequence of entity 2 (B), FASTA

>8G94_2 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains B)
MGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKSTIVKQMKIIHEAG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TTGIVETHFTFKDLHFKMFDVGAQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEM
NRMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAA
AYIQCQFEDLNKRKDTKEIYTHFTCSTDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 3 (C), FASTA

>8G94_3 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains C)
GPGSSGSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHL
AKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACG
GLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQ
QTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFF
PNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCN
VWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 4 (D), FASTA

>8G94_4 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains D)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 5 (E), FASTA

>8G94_5 scFv16 (chains E)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLELKAAAHHHHHHHH

Sequence of entity 6 (F, G), FASTA

>8G94_6 Early activation antigen CD69 (chains F, G)
MASENCFVAENSSLHPESGQENDATSPHFSTRHEGSFQVPVLCAVMNVVFITILIIALIA
LSVGQYNCPGQYTFSMPSDSHVSSCSEDWVGYQRKCYFISTVKRSWTSAQNACSEHGATL
AVIDSEKDMNFLKRYAGREEHWVGLKKEPGHPWKWSNGKEFNNWFNVTGSDKCVFLKNTE
VSSMECEKNLYWICNKPYKGSASWSHPQFEK

Primary citation

Transmembrane protein CD69 acts as an S1PR1 agonist. Chen, H., Qin, Y., Chou, M. et al. Elife (2023) 12. DOI 10.7554/eLife.88204 · PubMed

Other PDB entries of the same protein (UniProt P21453 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7TD4 2.6 Å, Sphingosine-1-phosphate receptor 1-Gi complex bound to Siponimod
9VNZ 2.79 Å, Cryo-EM structure of Gi coupled Sphingosine 1-phosphate receptor bound with HY-X-1011
9VO0 2.79 Å, Cryo-EM structure of Gi coupled Sphingosine 1-phosphate receptor bound with Ponesimod
3V2Y 2.8 Å, Crystal Structure of a Lipid G protein-Coupled Receptor at 2.80A
7VIF 2.83 Å, Cryo-EM structure of Gi coupled Sphingosine 1-phosphate receptor bound with (S)-FTY720-P
7EO4 2.86 Å, Cryo-EM of Sphingosine 1-phosphate receptor 1 / Gi complex bound to BAF312
7VIE 2.86 Å, Cryo-EM structure of Gi coupled Sphingosine 1-phosphate receptor bound with S1P
7EO2 2.89 Å, Cryo-EM of Sphingosine 1-phosphate receptor 1 / Gi complex bound to FTY720p
7VIG 2.89 Å, Cryo-EM structure of Gi coupled Sphingosine 1-phosphate receptor bound with CBP-307
9VO1 2.97 Å, Cryo-EM structure of Gi coupled Sphingosine 1-phosphate receptor bound with SAR247799
7EVY 2.98 Å, Cryo-EM structure of siponimod -bound Sphingosine-1-phosphate receptor 1 in complex with…
7VIH 2.98 Å, Cryo-EM structure of Gi coupled Sphingosine 1-phosphate receptor bound with CBP-307

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