9IYB: Prostaglandin D2 receptor 2

Cryo-EM Structure of the Prostaglandin D2 Receptor 2-PGD2 Coupled to G Protein. Determined by electron microscopy at 2.82 Å resolution. Released 4 Dec 2024.

Method: Electron microscopy
Resolution: 2.82 Å
Organisms: Homo sapiens, Rattus norvegicus
Chains: 5
Atoms: 8,992
Mol. weight: 157.11 kDa
Ligands: PG2, A1D5Q
Released: 4 Dec 2024

Explore 9IYB in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9IYB contains 37 α-helices and 62 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: 15 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	12-16	5
α-helix	35-38	4
α-helix	40-59	20
α-helix	65-81	17
α-helix	84-92	9
α-helix	101-134	34
α-helix	136-142	7
α-helix	145-168	24
β-strand	173-175	3	1
β-strand	179-181	3	1
α-helix	196-210	15
α-helix	211-216	6
α-helix	217-235	19
α-helix	239-241	3
α-helix	242-271	30
α-helix	278-304	27
α-helix	309-321	13

Chain B: 10 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	7-30	24
β-strand	34-40	7	2
α-helix	46-56	11
β-strand	185-191	7	2
β-strand	194-200	7	2
α-helix	208-210	3
α-helix	212-215	4
β-strand	220-225	6	2
α-helix	228-231	4
β-strand	233	1	3
β-strand	241	1	3
α-helix	242-254	13
β-strand	263-268	6	2
α-helix	271-278	8
α-helix	283-285	3
α-helix	296-308	13
β-strand	319-323	5	2
α-helix	329-350	22

Chain C: 4 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	5-25	21
α-helix	30-34	5
α-helix	38-43	6
β-strand	47-51	5	4
β-strand	58-63	6	5
β-strand	69-74	6	5
β-strand	78-83	6	5
β-strand	88-94	7	5
β-strand	100-105	6	6
β-strand	111-116	6	6
β-strand	120-125	6	6
β-strand	134-140	7	6
β-strand	146-150	5	7
β-strand	156-161	6	7
β-strand	166-170	5	7
β-strand	176-180	5	7
α-helix	186	1
β-strand	187-192	6	8
β-strand	198-203	6	8
β-strand	208-212	5	8
β-strand	218-222	5	8
β-strand	229-234	6	9
β-strand	240-245	6	9
β-strand	249-254	6	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	306-307	2	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	8-24	17
α-helix	30-44	15
α-helix	45-47	3
α-helix	53-55	3

Chain E: 4 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	11
β-strand	10-12	3	12
β-strand	18-25	8	11
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	78-83	6	11
α-helix	88-90	3
β-strand	92-99	8	12
β-strand	111	1	12
β-strand	115-119	5	12
β-strand	140-142	3	13
β-strand	146	1	14
β-strand	155-161	7	13
β-strand	166-167	2	15
β-strand	171-172	2	15
β-strand	174-179	6	14
β-strand	185-190	6	14
β-strand	194-195	2	14
α-helix	196	1
β-strand	203-208	6	13
β-strand	211-216	6	13
α-helix	221-223	3
β-strand	225-231	7	14
β-strand	239	1	14
β-strand	243-245	3	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Prostaglandin D2 receptor 2	A	protein	395	Homo sapiens	Q9Y5Y4 (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	248	Rattus norvegicus

Sequence of entity 1 (A), FASTA

>9IYB_1 Prostaglandin D2 receptor 2 (chains A)
MSANATLKPLCPILEQMSRLQSHSNTSIRYIDHAAVLLHGLASLLGLVENGVILFVVGCR
MRQTVVTTWVLHLALSDLLASASLPFFTYFLAVGHSWELGTTFCKLHSSIFFLNMFASGF
LLSAISLDRCLQVVRPVWAQNHRTVAAAHKVCLVLWALAVLNTVPYFVFRDTISRLDGRI
MCYYNVLLLNPGPDRDATCNSRQVALAVSKFLLAFLVPLAIIASSHAAVSLRLQHRGRRR
PGRFVRLVAAVVAAFALCWGPYHVFSLLEARAHANPGLRPLVWRGLPFVTSLAFFNSVAN
PVLYVLTCPDMLRKLRRSLRTVLESVLVDDSELGGAGSSRRRRTSSTARSASPLALCSRP
EEPRGPARLLGWLLGSCAASPQTGPLNRALSSTSS

Sequence of entity 2 (B), FASTA

>9IYB_2 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains B)
MGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKNTIVKQMKIIHEAG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TTGIVETHFTFKDLHFKMFDVGAQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEM
NRMHASMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAA
AYIQCQFEDLNKRKDTKEIYTHFTCSTDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 3 (C), FASTA

>9IYB_3 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains C)
MGSLLQSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHL
AKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACG
GLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQ
QTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFF
PNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCN
VWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 4 (D), FASTA

>9IYB_4 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains D)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 5 (E), FASTA

>9IYB_5 scFv16 (chains E)
MVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
AGGGGSGGGGSGGGGSADIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQ
RPGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTF
GAGTKLEL

Ligands and cofactors

ID	Name	Formula	Copies
PG2	Prostaglandin D2	C20 H32 O5	1
A1D5Q	[(2~{R})-1-hexadecanoyloxy-3-[oxidanyl-[(2~{S},3~{R},5~{R},6~{S})-2,3,4,5,6-pen…	C43 H81 O13 P	1

Primary citation

Molecular basis of lipid and ligand regulation of prostaglandin receptor DP2. Xu, J., Xu, Y., Hou, L. et al. Proc Natl Acad Sci U S A (2024) 121:e2403304121-e2403304121. DOI 10.1073/pnas.2403304121 · PubMed

Other PDB entries of the same protein (UniProt Q9Y5Y4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8XXV 2.33 Å, Cryo-EM Structure of the Prostaglandin D2 Receptor 2-indomethacin Coupled to G Protein
8XXU 2.54 Å, Cryo-EM Structure of the Prostaglandin D2 Receptor 2 Coupled to G Protein
7M8W 2.61 Å, XFEL crystal structure of the prostaglandin D2 receptor CRTH2 in complex with…
6D27 2.74 Å, Crystal structure of the prostaglandin D2 receptor CRTH2 with CAY10471
6D26 2.8 Å, Crystal structure of the prostaglandin D2 receptor CRTH2 with fevipiprant

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