7T6B: S1PR2-heterotrimeric G13 signaling complex

Structure of S1PR2-heterotrimeric G13 signaling complex. Determined by electron microscopy at 3.19 Å resolution. Released 6 Apr 2022.

Method: Electron microscopy
Resolution: 3.19 Å
Organisms: Homo sapiens, Mus musculus
Chains: 5
Atoms: 8,755
Mol. weight: 158.15 kDa
Ligands: S1P
Released: 6 Apr 2022

Explore 7T6B in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7T6B contains 25 α-helices and 64 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: 6 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	7-28	22
β-strand	49-54	6	1
α-helix	61-71	11
β-strand	209-213	5	1
β-strand	216-222	7	1
β-strand	244-248	5	1
β-strand	255	1	2
β-strand	263	1	2
α-helix	264-276	13
β-strand	287-291	5	1
α-helix	293-298	6
α-helix	320-331	12
β-strand	343-344	2	1
α-helix	353-373	21

Chain C: 2 helices, 32 β-strands

Element	Residues	Length	Sheet
α-helix	4-25	22
α-helix	38-39	2
β-strand	47-52	6	3
β-strand	58-63	6	4
β-strand	69	1	5
β-strand	70-74	5	4
β-strand	78-82	5	4
β-strand	83	1	5
β-strand	89-94	6	4
β-strand	100-103	4	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	157-161	5	7
β-strand	165-169	5	7
β-strand	176-181	6	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	250-254	5	9
β-strand	259-264	6	9
β-strand	273-278	6	10
β-strand	284-289	6	10
β-strand	294-298	5	10
β-strand	304-308	5	10
β-strand	315	1	11
β-strand	319-320	2	3
β-strand	327-330	4	3
β-strand	331	1	11
β-strand	335-339	5	3

Chain D: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	8-23	16
α-helix	30-43	14
α-helix	53-55	3

Chain E: 4 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	12
β-strand	10-12	3	13
β-strand	17-25	9	12
α-helix	29-31	3
β-strand	33-39	7	14
β-strand	45-51	7	14
β-strand	58-60	3	14
β-strand	69-73	5	12
β-strand	78-84	7	12
α-helix	88-90	3
β-strand	92-94	3	13
β-strand	95-99	5	14
β-strand	111	1	14
β-strand	115-119	5	13
β-strand	141-142	2	15
β-strand	146-148	3	16
β-strand	155-160	6	15
β-strand	166	1	17
β-strand	172	1	17
β-strand	174-179	6	16
β-strand	186-190	5	16
β-strand	194-195	2	16
α-helix	196	1
β-strand	203-207	5	15
β-strand	212-216	5	15
β-strand	226-231	6	16
α-helix	237	1
β-strand	243-246	4	16

Chain R: 10 helices, 0 β-strands

Element	Residues	Length
α-helix	14-20	7
α-helix	34-60	27
α-helix	68-90	23
α-helix	91-93	3
α-helix	102-135	34
α-helix	147-168	22
α-helix	190-217	28
α-helix	235-258	24
α-helix	267-269	3
α-helix	270-287	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Guanine nucleotide-binding protein subunit alpha-13	A	protein	362	Homo sapiens	P63096 (AlphaFold model), Q14344 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	C	protein	362	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
Sphingosine 1-phosphate receptor 2	R	protein	361	Homo sapiens	O95136

Sequence of entity 1 (A), FASTA

>7T6B_1 Guanine nucleotide-binding protein subunit alpha-13 (chains A)
MGCTLSAEDKAAVERSKMIDRNLREDGEKAARLVKILLLGAGESGKSTFLKQMRIIHGQD
FDQRAREEFRPTIYSNVIKGMRVLVDAREKLHIPWGDNSNQQHGDKMMSFDTRAPMAAQG
MVETRVFLQYLPAIRALWADSGIQNAYDRRREFQLGESVKYFLDNLDKLGEPDYIPSQQD
ILLARRPTKGIHEYDFEIKNVPFKMVDVGGQRSERKRWFECFDSVTSILFLVSSSEFDQV
LMEDRLTNRLTESLNIFETIVNNRVFSNVSIILFLNKTDLLEEKVQVVSIKDYFLEFEGD
PHCLRDVQKFLVECFRGKRRDQQQKPLYHHFTTAINTENIRLVFRDVKDTILHDNLKQLM
LQ

Sequence of entity 2 (C), FASTA

>7T6B_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains C)
MHHHHHHHHHHLEVLFQGPGSSGSELDQLRQEAEQLKNQIRDARKACADATLSQITNNID
PVGRIQMRTRRTLRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSS
WVMTCAYAPSGNYVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIV
TSSGDTTCALWDIETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMC
RQTFTGHESDINAICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSF
SKSGRLLLAGYDDFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKI
WN

Sequence of entity 3 (D), FASTA

>7T6B_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains D)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 4 (E), FASTA

>7T6B_4 scFv16 (chains E)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLELKAAAHHHHHHHH

Sequence of entity 5 (R), FASTA

>7T6B_5 Sphingosine 1-phosphate receptor 2 (chains R)
MGSLYSEYLNPNKVQEHYNYTKETLETQETTSRQVASAFIVILCCAIVVENLLVLIAVAR
NSKFHSAMYLFLGNLAASDLLAGVAFVANTLLSGSVTLRLTPVQWFAREGSAFITLSASV
FSLLAIAIERHVAIAKVKLYGSDKSCRMLLLIGASWLISLVLGGLPILGWNCLGHLEACS
TVLPLYAKHYVLCVVTIFSIILLAIVALYVRIYCVVRSSHADMAAPQTLALLKTVTIVLG
VFIVCWLPAFSILLLDYACPVHSCPILYKAHYFFAVSTLNSLLNPVIYTWRSRDLRREVL
RPLQCWRPGVGVQGRRRGGTPGHHLLPLRSSSSLERGMHMPTSPTFLEGNTVVDYKDDDD
K

Ligands and cofactors

ID	Name	Formula	Copies
S1P	(2S,3R,4E)-2-amino-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate	C18 H38 N O5 P	1

Primary citation

Structure of S1PR2-heterotrimeric G 13 signaling complex. Chen, H., Chen, K., Huang, W. et al. Sci Adv (2022) 8:eabn0067-eabn0067. DOI 10.1126/sciadv.abn0067 · 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…

Browse structure collections

About this viewer

MolViewer shows 7T6B directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.