8YH3: A3R-Gi complex
A3R-Gi complex bound to m6A. Determined by electron microscopy at 3.4 Å resolution. Released 6 Nov 2024.
- Method
- Electron microscopy
- Resolution
- 3.4 Å
- Organisms
- Rattus rattus, Influenza A virus (A/Victoria/3/1975(H3N2)), Ovis aries
- Chains
- 5
- Atoms
- 8,691
- Mol. weight
- 254.6 kDa
- Ligands
- 6MD
- Released
- 6 Nov 2024
Explore 8YH3 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8YH3 contains 36 α-helices and 61 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: 7 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 9-30 | 22 | |
| β-strand | 33-40 | 8 | 9 |
| α-helix | 46-52 | 7 | |
| β-strand | 185-191 | 7 | 9 |
| β-strand | 194-200 | 7 | 9 |
| α-helix | 212-215 | 4 | |
| β-strand | 220-224 | 5 | 9 |
| α-helix | 242-255 | 14 | |
| β-strand | 264-267 | 4 | 9 |
| α-helix | 276-278 | 3 | |
| α-helix | 296-309 | 14 | |
| β-strand | 319-320 | 2 | 9 |
| α-helix | 331-348 | 18 | |
Chain B: 2 helices, 28 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-25 | 19 | |
| α-helix | 30-33 | 4 | |
| 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 | 100-105 | 6 | 3 |
| β-strand | 111-116 | 6 | 3 |
| β-strand | 120-125 | 6 | 3 |
| β-strand | 134-140 | 7 | 3 |
| β-strand | 146-153 | 8 | 4 |
| β-strand | 156-161 | 6 | 4 |
| β-strand | 166-170 | 5 | 4 |
| β-strand | 176-180 | 5 | 4 |
| β-strand | 187-192 | 6 | 5 |
| β-strand | 198-203 | 6 | 5 |
| β-strand | 208-212 | 5 | 5 |
| β-strand | 218-222 | 5 | 5 |
| β-strand | 229-234 | 6 | 6 |
| β-strand | 240-245 | 6 | 6 |
| β-strand | 250-254 | 5 | 6 |
| β-strand | 260-264 | 5 | 6 |
| β-strand | 273-278 | 6 | 7 |
| β-strand | 284-289 | 6 | 7 |
| β-strand | 294-298 | 5 | 7 |
| β-strand | 304-307 | 4 | 7 |
| β-strand | 317-320 | 4 | 1 |
| β-strand | 327-330 | 4 | 1 |
| β-strand | 336-339 | 4 | 1 |
Chain G: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 10-23 | 14 | |
| α-helix | 30-43 | 14 | |
| α-helix | 53-55 | 3 | |
Chain R: 19 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 | 8 |
| 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 | 8 |
| 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 | 282-284 | 3 | |
| α-helix | 286-294 | 9 | |
Chain S: 5 helices, 25 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-7 | 5 | 10 |
| β-strand | 10-12 | 3 | 11 |
| β-strand | 18-25 | 8 | 10 |
| α-helix | 29-31 | 3 | |
| β-strand | 33-40 | 8 | 11 |
| β-strand | 44-51 | 8 | 11 |
| β-strand | 58-60 | 3 | 11 |
| α-helix | 62-64 | 3 | |
| β-strand | 69-71 | 3 | 10 |
| β-strand | 78-83 | 6 | 10 |
| α-helix | 88-90 | 3 | |
| β-strand | 92-99 | 8 | 11 |
| β-strand | 111 | 1 | 11 |
| β-strand | 115-119 | 5 | 11 |
| β-strand | 128-130 | 3 | 12 |
| β-strand | 134-136 | 3 | 13 |
| β-strand | 143-149 | 7 | 12 |
| β-strand | 154 | 1 | 14 |
| β-strand | 160 | 1 | 14 |
| β-strand | 162 | 1 | 15 |
| β-strand | 164-167 | 4 | 13 |
| β-strand | 173-177 | 5 | 13 |
| β-strand | 183 | 1 | 13 |
| β-strand | 191-196 | 6 | 12 |
| β-strand | 199-204 | 6 | 12 |
| α-helix | 209-211 | 3 | |
| β-strand | 214-216 | 3 | 13 |
| β-strand | 219 | 1 | 15 |
| α-helix | 225 | 1 | |
| β-strand | 231-234 | 4 | 13 |
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) |
| 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) |
| 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) |
Sequence of entity 1 (B), FASTA
>8YH3_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 (R), FASTA
>8YH3_2 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 3 (A, G), FASTA
>8YH3_3 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 4 (S), FASTA
>8YH3_4 scfv16 (chains S)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLELKAAAASSEDLYFQ
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| 6MD | N-methyladenosine | C11 H15 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
Browse structure collections
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