9EBH: Human adenosine A3 receptor Gi1 complex

Human adenosine A3 receptor Gi1 complex bound to adenosine. Determined by electron microscopy at 3.6 Å resolution. Released 20 Aug 2025.

Method: Electron microscopy
Resolution: 3.6 Å
Organisms: Homo sapiens, Mus musculus
Chains: 5
Atoms: 8,612
Mol. weight: 154.48 kDa
Ligands: ADN
Released: 20 Aug 2025

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

Secondary structure: helices and β-sheets

9EBH contains 42 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: 9 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	7-32	26
β-strand	34-39	6	1
α-helix	47-53	7
β-strand	185-190	6	1
β-strand	195-200	6	1
α-helix	208-210	3
α-helix	212-215	4
β-strand	220-226	7	1
α-helix	242-254	13
β-strand	263-269	7	1
α-helix	271-280	10
α-helix	283-285	3
α-helix	296-309	14
β-strand	319-323	5	1
α-helix	330-351	22

Chain B: 3 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	8-25	18
α-helix	30-34	5
β-strand	47-51	5	2
β-strand	58-63	6	3
β-strand	69-74	6	3
β-strand	78-83	6	3
β-strand	88-94	7	3
β-strand	100-105	6	4
β-strand	111-116	6	4
β-strand	121-125	5	4
β-strand	134-139	6	4
β-strand	148-151	4	5
β-strand	157-160	4	5
β-strand	165-168	4	5
β-strand	178-181	4	5
α-helix	186-187	2
β-strand	189-192	4	6
β-strand	198-202	5	6
β-strand	207-212	6	6
β-strand	218-223	6	6
β-strand	229-234	6	7
β-strand	240-245	6	7
β-strand	249-254	6	7
β-strand	260-265	6	7
β-strand	273-278	6	8
β-strand	284-289	6	8
β-strand	294-298	5	8
β-strand	303-308	6	8
β-strand	315-320	6	2
β-strand	327-331	5	2
β-strand	336-339	4	2

Chain E: 4 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	9
β-strand	18-25	8	9
α-helix	29-31	3
β-strand	33-39	7	10
β-strand	45-51	7	10
β-strand	58-60	3	10
β-strand	65	1	9
β-strand	68-73	6	9
β-strand	78-83	6	9
β-strand	93-99	7	10
β-strand	110-111	2	10
β-strand	115-116	2	10
α-helix	137-140	4
β-strand	141-142	2	11
β-strand	146-148	3	12
β-strand	155-160	6	11
β-strand	166	1	13
β-strand	172	1	13
β-strand	174-179	6	12
β-strand	185-189	5	12
β-strand	203-206	4	11
β-strand	211-216	6	11
α-helix	221-223	3
β-strand	226-231	6	12
α-helix	237	1
β-strand	238	1	10
β-strand	239	1	12
β-strand	243-246	4	12

Chain G: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	10-13	4
α-helix	15-23	9
α-helix	30-43	14
α-helix	45-47	3
α-helix	53-55	3

Chain R: 21 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	12-39	28
α-helix	41-43	3
α-helix	47-60	14
α-helix	61-65	5
α-helix	66-74	9
β-strand	77	1	14
α-helix	80-113	34
α-helix	115-117	3
α-helix	118-121	4
α-helix	124-141	18
α-helix	145-147	3
α-helix	151-153	3
α-helix	157-160	4
β-strand	165	1	14
α-helix	168-171	4
α-helix	174-176	3
α-helix	177-187	11
α-helix	188-205	18
α-helix	227-254	28
α-helix	261-276	16
α-helix	278	1
α-helix	279-283	5
α-helix	287-292	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Guanine nucleotide-binding protein G(i) subunit alpha-1	A	protein	354	Homo sapiens	P63096 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	349	Homo sapiens	P62873 (AlphaFold model)
Antibody fragment scFv16\|Mus musculus (10090)	E	protein	248	Mus musculus
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	G	protein	70	Homo sapiens	P59768 (AlphaFold model)
Adenosine receptor A3	R	protein	363	Homo sapiens	P0DMS8 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9EBH_1 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains A)
MGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKNTIVKQMKIIHEAG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TTGIVETHFTFKDLHFKMFDVGAQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEM
NRMHASMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAA
AYIQCQFEDLNKRKDTKEIYTHFTCSTDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 2 (B), FASTA

>9EBH_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
HHHHHHGSSGSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTL
RGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNY
VACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDI
ETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINA
ICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDD
FNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 3 (E), FASTA

>9EBH_3 Antibody fragment scFv16|Mus musculus (10090) (chains E)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLELK

Sequence of entity 4 (G), FASTA

>9EBH_4 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
ASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENPF
REKKFFCAIL

Sequence of entity 5 (R), FASTA

>9EBH_5 Adenosine receptor A3 (chains R)
DYKDDDDAANFTPVNGSSGNQSVRLVTSSSLEVLFQGPPNNSTALSLANVTYITMEIFIG
LCAIVGNVLVICVVKLNPSLQTTTFYFIVSLALADIAVGVLVMPLAIVVSLGITIHFYSC
LFMTCLLLIFTHASIMSLLAIAVDRYLRVKLTVRYKRVTTHRRIWLALGLCWLVSFLVGL
TPMFGWNMKLTSEYHRNVTFLSCQFVSVMRMDYMVYFSFLTWIFIPLVVMCAIYLDIFYI
IRNKLSLNLSNSKETGAFYGREFKTAKSLFLVLFLFALSWLPLSIINCIIYFNGEVPQLV
LYMGILLSHANSMMNPIVYAYKIKKFKETYLLILKACVVCHPSDSLDTSIEKNSEHHHHH
HHH

Ligands and cofactors

ID	Name	Formula	Copies
ADN	Adenosine	C10 H13 N5 O4	1

Primary citation

Molecular basis of ligand binding and receptor activation at the human A 3 adenosine receptor. Zhang, L., Mobbs, J.I., Bennetts, F.M. et al. Nat Commun (2025) 16:7674-7674. DOI 10.1038/s41467-025-62872-x · 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…

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