7LD3: Human adenosine A1 receptor-Gi2-protein complex

Cryo-EM structure of the human adenosine A1 receptor-Gi2-protein complex bound to its endogenous agonist and an allosteric ligand. Determined by electron microscopy at 3.2 Å resolution. Released 8 Sept 2021.

Method: Electron microscopy
Resolution: 3.2 Å
Organism: Homo sapiens
Chains: 4
Atoms: 7,016
Mol. weight: 130.88 kDa
Ligands: XTD, ADN
Released: 8 Sept 2021

Explore 7LD3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7LD3 contains 35 α-helices and 36 β-strands across 4 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	12-29	18
β-strand	33-40	8	1
α-helix	46-52	7
β-strand	186-192	7	1
β-strand	195-201	7	1
α-helix	209-211	3
α-helix	213-216	4
β-strand	221-227	7	1
α-helix	229-231	3
α-helix	243-255	13
β-strand	264-270	7	1
α-helix	272-281	10
α-helix	297-309	13
β-strand	320-324	5	1
α-helix	329-352	24

Chain B: 5 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	5-24	20
α-helix	30-33	4
α-helix	38-39	2
α-helix	45-46	2
β-strand	47-51	5	3
β-strand	58-63	6	4
β-strand	69-74	6	4
β-strand	78-83	6	4
β-strand	89-94	6	4
α-helix	95	1
β-strand	100-105	6	5
β-strand	111-116	6	5
β-strand	121-125	5	5
β-strand	134-139	6	5
β-strand	146-151	6	6
β-strand	156-161	6	6
β-strand	166-170	5	6
β-strand	175-180	6	6
β-strand	187-192	6	7
β-strand	198-203	6	7
β-strand	208-212	5	7
β-strand	217-222	6	7
β-strand	229-234	6	8
β-strand	240-245	6	8
β-strand	250-254	5	8
β-strand	259-264	6	8
β-strand	273-278	6	9
β-strand	284-289	6	9
β-strand	294-298	5	9
β-strand	304-308	5	9
β-strand	315-320	6	3
β-strand	327-331	5	3
β-strand	336-339	4	3

Chain G: 4 helices, 0 β-strands

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

Chain R: 17 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	7-35	29
α-helix	43-61	19
α-helix	63-71	9
β-strand	74-76	3	2
α-helix	77-110	34
α-helix	121-139	19
α-helix	141-143	3
α-helix	149-159	11
β-strand	166-168	3	2
α-helix	171-174	4
α-helix	177-178	2
α-helix	179-185	7
α-helix	186-188	3
α-helix	190-210	21
α-helix	226-259	34
α-helix	267-278	12
α-helix	284	1
α-helix	285-289	5
α-helix	293-299	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Guanine nucleotide-binding protein G(i) subunit alpha-2	A	protein	355	Homo sapiens	P04899 (AlphaFold model)
Chimera protein of Muscarinic acetylcholine receptor M4 and Adenosine receptor A1	R	protein	387	Homo sapiens	P08173 (AlphaFold model), P30542 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	350	Homo sapiens	P62873 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	G	protein	71	Homo sapiens	P59768

Sequence of entity 1 (A), FASTA

>7LD3_1 Guanine nucleotide-binding protein G(i) subunit alpha-2 (chains A)
MGCTVSAEDKAAAERSKMIDKNLREDGEKAAREVKLLLLGAGESGKNTIVKQMKIIHEDG
YSEEECRQYRAVVYSNTIQSIMAIVKAMGNLQIDFADPSRADDARQLFALSCTAEEQGVL
PDDLSGVIRRLWADHGVQACFGRSREYQLNDSAAYYLNDLERIAQSDYIPTQQDVLRTRV
KTTGIVETHFTFKDLHFKMFDVGAQRSERKKWIHCFEGVTAIIFCVALSAYDLVLAEDEE
MNRMHASMKLFDSICNNKWFTDTSIILFLNKKDLFEEKITHSPLTICFPEYTGANKYDEA
ASYIQSKFEDLNKRKDTKEIYTHFTCSTDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 2 (R), FASTA

>7LD3_2 Chimera protein of Muscarinic acetylcholine receptor M4 and Adenosine receptor A1 (chains R)
MKTIIALSYIFCLVFADYKDDDDAMGANFTPVNGSSGNQSVRLVTSSSLEVLFQGPPPSI
SAFQAAYIGIEVLIALVSVPGNVLVIWAVKVNQALRDATFCFIVSLAVADVAVGALVIPL
AILINIGPQTYFHTCLMVACPVLILTQSSILALLAIAVDRYLRVKIPLRYKMVVTPRRAA
VAIAGCWILSFVVGLTPMFGWNNLSAVERAWAANGSMGEPVIKCEFEKVISMEYMVYFNF
FVWVLPPLLLMVLIYLEVFYLIRKQLNKKVSASSGDPQKYYGKELKIAKSLALILFLFAL
SWLPLHILNCITLFCPSCHKPSILTYIAIFLTHGNSAMNPIVYAFRIQKFRVTFLKIWND
HFRCQPAPPIDEDLPEERPDDHHHHHH

Sequence of entity 3 (B), FASTA

>7LD3_3 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
MHHHHHHGSSGSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRT
LRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGN
YVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWD
IETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDIN
AICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYD
DFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 4 (G), FASTA

>7LD3_4 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Ligands and cofactors

ID	Name	Formula	Copies
XTD	{2-amino-4-[3,5-bis(trifluoromethyl)phenyl]thiophen-3-yl}(4-chlorophenyl)methan…	C19 H10 Cl F6 N O S	1
ADN	Adenosine	C10 H13 N5 O4	1

Primary citation

Positive allosteric mechanisms of adenosine A 1 receptor-mediated analgesia. Draper-Joyce, C.J., Bhola, R., Wang, J. et al. Nature (2021) 597:571-576. DOI 10.1038/s41586-021-03897-2 · PubMed

Other PDB entries of the same protein (UniProt P04899 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8ZBW 2.58 Å, Cryo-EM structure of formyl peptide receptor 2/C1R receptor in complex with Gi
8THK 2.6 Å, Cryo-EM structure of A61603-bound alpha-1A-adrenergic receptor in complex with…
7YK7 2.75 Å, Cryo-EM structure of the DC591053-bound human relaxin family peptide receptor 4…
9K6L 2.77 Å, Cryo-EM structure of GPCR16-Gi2 complex
9XDQ 2.79 Å, Cryo-EM structure of BMS986187 bound DOR-Gi complex
7WVX 2.8 Å, Cryo-EM structure of the human formyl peptide receptor 2 in complex with fhumanin and Gi2
8W8A 2.8 Å, Cryo-EM structure of the RO5256390-TAAR1 complex
8ZSJ 2.8 Å, Cryo-EM structure of the apo hTAAR1-Gs complex
7WVV 2.9 Å, Cryo-EM structure of the human formyl peptide receptor 2 in complex with fMLFII and Gi2
9DQJ 2.9 Å, CryoEM structure of Gq-coupled MRGPRD with a new agonist EP-3945
9KFI 2.91 Å, Cryo-EM structure of the human relaxin family peptide receptor 3 in complex with…
9KFK 2.95 Å, Cryo-EM structure of the relaxin-3-bound human relaxin family peptide receptor 4…

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