8YH2: A3R-Gi complex

A3R-Gi complex bound to adenosine. Determined by electron microscopy at 3.27 Å resolution. Released 6 Nov 2024.

Method: Electron microscopy
Resolution: 3.27 Å
Organisms: Rattus rattus, Homo sapiens, Influenza A virus (A/Victoria/3/1975(H3N2))
Chains: 5
Atoms: 8,690
Mol. weight: 254.58 kDa
Ligands: ADN
Released: 6 Nov 2024

Explore 8YH2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8YH2 contains 35 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: 6 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	9-30	22
β-strand	33-40	8	10
α-helix	46-52	7
β-strand	185-191	7	10
β-strand	194-200	7	10
α-helix	212-215	4
β-strand	220-224	5	10
α-helix	242-255	14
β-strand	263-267	5	10
α-helix	296-309	14
β-strand	319-322	4	10
α-helix	331-351	21

Chain B: 3 helices, 30 β-strands

Element	Residues	Length	Sheet
α-helix	7-25	19
α-helix	30-33	4
α-helix	38-39	2
β-strand	47-51	5	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	104-105	2	3
β-strand	111-113	3	3
β-strand	116	1	4
β-strand	120	1	4
β-strand	123-125	3	3
β-strand	134-137	4	3
β-strand	146-153	8	5
β-strand	156-161	6	5
β-strand	165-169	5	5
β-strand	176-181	6	5
β-strand	187-192	6	6
β-strand	198-203	6	6
β-strand	208-212	5	6
β-strand	218-222	5	6
β-strand	229-234	6	7
β-strand	241-245	5	7
β-strand	250-253	4	7
β-strand	260-264	5	7
β-strand	273-278	6	8
β-strand	285-289	5	8
β-strand	294-297	4	8
β-strand	304-307	4	8
β-strand	315-320	6	1
β-strand	327-331	5	1
β-strand	336-339	4	1

Chain G: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	10-23	14
α-helix	30-43	14
α-helix	53-55	3

Chain R: 18 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	10-39	30
α-helix	41-43	3
α-helix	46-63	18
α-helix	65-74	10
β-strand	77	1	9
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	151-154	4
β-strand	164	1	9
α-helix	167-170	4
α-helix	173-174	2
α-helix	175-181	7
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: 5 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
α-helix	29-31	3
β-strand	33-40	8	12
β-strand	44-51	8	12
α-helix	53-55	3
β-strand	58-60	3	12
β-strand	69-73	5	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	128-130	3	13
β-strand	134-136	3	14
β-strand	143-149	7	13
β-strand	154	1	15
β-strand	160	1	15
β-strand	162-167	6	14
β-strand	175-177	3	14
β-strand	183	1	14
β-strand	191-196	6	13
β-strand	199-204	6	13
α-helix	209-211	3
β-strand	214-219	6	14
α-helix	225	1
β-strand	226	1	14
β-strand	231-234	4	14

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	P63096 (AlphaFold model)
Hemagglutinin,Adenosine receptor A3,GFP chimera	R	protein	794	Influenza A virus (A/Victoria/3/1975(H3N2)), Ovis aries, Human orthopneumovirus	P35342 (AlphaFold model)
scfv16	S	protein	260	Mus musculus	A0A0B4J1H6 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>8YH2_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

>8YH2_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 (R), FASTA

>8YH2_3 Hemagglutinin,Adenosine receptor A3,GFP chimera (chains R)
MKTIIALSYIFCLVFADYKDDDDAMGPVNSTAVSWTSVTYITVEILIGLCAIVGNVLVIW
VVKLNPSLQTTTFYFIVSLALADIAVGVLVMPLAIVISLGVTIHFYSCLFMTCLMLIFTH
ASIMSLLAIAVDRYLRVKLTVRYRRVTTQRRIWLALGLCWLVSFLVGLTPMFGWNMKLSS
ADENLTFLPCRFRSVMRMDYMVYFSFFLWILVPLVVMCAIYFDIFYIIRNRLSQSFSGSR
ETGAFYGREFKTAKSLLLVLFLFALCWLPLSIINCILYFDGQVPQTVLYLGILLSHANSM
MNPIVYAYKIKKFKETYLLILKACVICQPSKSMDPSTEQTSEGSGGGGSGGSSSGGVFTL
EDFVGDWEQTAAYNLDQVLEQGGVSSLLQNLAVSVTPIQRIVRSGENALKIDIHVIIPYE
GLSADQMAQIEEVFKVVYPVDDHHFKVILPYGTLVIDGVTPNMLNYFGRPYEGIAVFDGK
KITVTGTLWNGNKIIDERLITPDGSMLFRVTINSGGSGGGGSGGSSSGGLEVLFQGPGSA
AAAVSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPW
PTLVTTLTYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGD
TLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQ
LADHYQQNTPIGDGPVLLPDNHYLSTQSKLSKDPNEKRDHMVLLEFVTAAGITLGMDELY
KSGLRSHHHHHHHH

Sequence of entity 4 (S), FASTA

>8YH2_4 scfv16 (chains S)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLELKAAAASSEDLYFQ

Ligands and cofactors

ID	Name	Formula	Copies
ADN	Adenosine	C10 H13 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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