8YH5: A3R-Gi complex

A3R-Gi complex bound to i6A. Determined by electron microscopy at 3.66 Å resolution. Released 6 Nov 2024.

Method: Electron microscopy
Resolution: 3.66 Å
Organisms: Rattus rattus, Homo sapiens, Bos taurus
Chains: 5
Atoms: 8,695
Mol. weight: 254.65 kDa
Ligands: ZIR
Released: 6 Nov 2024

Explore 8YH5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8YH5 contains 34 α-helices and 60 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: 8 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	7-30	24
β-strand	34-39	6	13
α-helix	46-52	7
β-strand	185-191	7	13
β-strand	194-200	7	13
α-helix	201-203	3
α-helix	212-215	4
β-strand	221-224	4	13
α-helix	242-255	14
β-strand	264-267	4	13
α-helix	276-280	5
α-helix	296-309	14
β-strand	319-322	4	13
α-helix	331-351	21

Chain B: 2 helices, 29 β-strands

Element	Residues	Length	Sheet
α-helix	7-24	18
α-helix	30-34	5
β-strand	47-52	6	1
β-strand	58-63	6	2
β-strand	69-74	6	2
β-strand	78-83	6	2
β-strand	88-94	7	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	1	5
β-strand	222-223	2	5
β-strand	229-234	6	6
β-strand	240-245	6	6
β-strand	250-254	5	6
β-strand	260-263	4	6
β-strand	273-278	6	7
β-strand	284-289	6	7
β-strand	294-298	5	7
β-strand	304-308	5	7
β-strand	315-320	6	1
β-strand	327-331	5	1
β-strand	335-339	5	1

Chain G: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	13-23	11
α-helix	34-43	10
α-helix	54-55	2

Chain R: 17 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	10-39	30
α-helix	46-63	18
α-helix	65-74	10
β-strand	77	1	14
α-helix	80-114	35
α-helix	115-117	3
α-helix	118-121	4
α-helix	124-143	20
α-helix	144-147	4
α-helix	151-153	3
β-strand	164	1	14
α-helix	167-170	4
α-helix	173-175	3
α-helix	176-181	6
α-helix	182-184	3
α-helix	186-206	21
α-helix	225-253	29
α-helix	260-281	22
α-helix	286-294	9

Chain S: 4 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	8
β-strand	10-12	3	9
β-strand	19-25	7	8
α-helix	29-31	3
β-strand	33-40	8	9
β-strand	44-51	8	9
α-helix	53-55	3
β-strand	58-60	3	9
β-strand	68-73	6	8
β-strand	78-83	6	8
β-strand	92-99	8	9
β-strand	111	1	9
β-strand	115-119	5	9
β-strand	129-130	2	10
β-strand	135-136	2	11
β-strand	143-148	6	10
β-strand	154	1	12
β-strand	160	1	12
β-strand	162-167	6	11
β-strand	175-177	3	11
β-strand	183	1	11
β-strand	191-196	6	10
β-strand	199-204	6	10
α-helix	209-211	3
β-strand	213-219	7	11
α-helix	225	1
β-strand	232-234	3	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	375	Rattus rattus	P54311 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2,Guanine nucleotide-binding…	A, G	protein	433	Homo sapiens, Bos taurus	P63096 (AlphaFold model)
scfv16	S	protein	260	Mus musculus	A0A0B4J1H6 (AlphaFold model)
Hemagglutinin,Adenosine receptor A3,GFP chimera	R	protein	794	Influenza A virus (A/Victoria/3/1975(H3N2)), Ovis aries, human respiratory syncytial virus	P35342 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>8YH5_1 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
MGSLLQSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHL
AKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACG
GLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQ
QTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFF
PNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCN
VWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWNGASGGGSGGNSGSSG
GSSGVSGWRLFKKIS

Sequence of entity 2 (A, G), FASTA

>8YH5_2 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2,Guanine nucleotide-binding protein G(i) subunit alpha-1 chimera (chains A, G)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAILGSAGSAGSAMCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGA
GESGKSTIVKQMKIIHEAGYSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARA
DDARQLFVLAGAAEEGFMTAELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDR
IAQPNYIPTQQDVLRTRVKTTGIVETHFTFKDLHFKMFDVGGQRSERKKWIHCFEGVTAI
IFCVALSDYDLVLAEDEEMNRMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKS
PLTICYPEYAGSNTYEEAAAYIQCQFEDLNKRKDTKEIYTHFTCATDTKNVQFVFDAVTD
VIIKNNLKDCGLF

Sequence of entity 3 (S), FASTA

>8YH5_3 scfv16 (chains S)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLELKAAAASSEDLYFQ

Sequence of entity 4 (R), FASTA

>8YH5_4 Hemagglutinin,Adenosine receptor A3,GFP chimera (chains R)
MKTIIALSYIFCLVFADYKDDDDAMGPVNSTAVSWTSVTYITVEILIGLCAIVGNVLVIW
VVKLNPSLQTTTFYFIVSLALADIAVGVLVMPLAIVISLGVTIHFYSCLFMTCLMLIFTH
ASIMSLLAIAVDRYLRVKLTVRYRRVTTQRRIWLALGLCWLVSFLVGLTPMFGWNMKLSS
ADENLTFLPCRFRSVMRMDYMVYFSFFLWILVPLVVMCAIYFDIFYIIRNRLSQSFSGSR
ETGAFYGREFKTAKSLLLVLFLFALCWLPLSIINCILYFDGQVPQTVLYLGILLSHANSM
MNPIVYAYKIKKFKETYLLILKACVICQPSKSMDPSTEQTSEGSGGGGSGGSSSGGVFTL
EDFVGDWEQTAAYNLDQVLEQGGVSSLLQNLAVSVTPIQRIVRSGENALKIDIHVIIPYE
GLSADQMAQIEEVFKVVYPVDDHHFKVILPYGTLVIDGVTPNMLNYFGRPYEGIAVFDGK
KITVTGTLWNGNKIIDERLITPDGSMLFRVTINSGGSGGGGSGGSSSGGLEVLFQGPGSA
AAAVSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPW
PTLVTTLTYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGD
TLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQ
LADHYQQNTPIGDGPVLLPDNHYLSTQSKLSKDPNEKRDHMVLLEFVTAAGITLGMDELY
KSGLRSHHHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
ZIR	N-(3-methylbut-2-en-1-yl)adenosine	C15 H21 N5 O4	1

Primary citation

Structural insights into the agonist selectivity of the adenosine A 3 receptor. Oshima, H.S., Ogawa, A., Sano, F.K. et al. Nat Commun (2024) 15:9294-9294. DOI 10.1038/s41467-024-53473-1 · PubMed

Other PDB entries of the same protein (UniProt P54311 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7MBX 1.95 Å, Human Cholecystokinin 1 receptor (CCK1R) Gs complex
9EJZ 2.06 Å, Human M5 muscarinic acetylcholine receptor complex with mini-Gq, agonist acetylcholine…
9IJE 2.34 Å, Epinephrine-activated human beta3 adrenergic receptor
8YK0 2.4 Å, Cryo-EM structure of human GPR156-Gi3 complex
8Z9O 2.4 Å, Cryo-EM structure of human GPR4-Gs complex
22ES 2.43 Å, Gi bound kappa-opioid receptor in complex with difelikefalin
7MBY 2.44 Å, Human Cholecystokinin 1 receptor (CCK1R) Gq chimera (mGsqi) complex
9WG6 2.44 Å, D1R-Gs in complexed with Dopamine/LY3154207/BMSA1/UNC9815
8JIS 2.46 Å, Cryo-EM structure of the GLP-1R/GCGR dual agonist peptide15-bound human GLP-1R-Gs complex
9M0R 2.47 Å, Structure of neuropeptide FF receptor 1 complex with NPVF
8YKV 2.48 Å, Cryo-EM structure of succinate receptor SUCR1 bound to compound 31
9M1O 2.49 Å, Cryo-EM structures of NPFFR2 complex with neuropeptide FF

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