8WJX: ADP-bound purinergic receptor 1

ADP-bound purinergic receptor 1 in complex with miniGs/q. Determined by electron microscopy at 3.2 Å resolution. Released 2 Oct 2024.

Method: Electron microscopy
Resolution: 3.2 Å
Organisms: Homo sapiens, Escherichia coli
Chains: 5
Atoms: 7,535
Mol. weight: 174.22 kDa
Ligands: CLR, ADP
Released: 2 Oct 2024

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

Secondary structure: helices and β-sheets

8WJX contains 33 α-helices and 50 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: 10 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	10-39	30
β-strand	40-47	8	1
α-helix	53-61	9
β-strand	207-210	4	1
β-strand	213-214	2	1
β-strand	217-224	8	1
α-helix	231-235	5
α-helix	236-239	4
β-strand	243-247	5	1
β-strand	249	1	2
α-helix	256-268	13
β-strand	276-281	6	1
β-strand	282	1	2
α-helix	284-293	10
α-helix	298-301	4
α-helix	303-305	3
α-helix	322-341	20
β-strand	349-353	5	1
α-helix	361-380	20

Chain B: 3 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	13-25	13
α-helix	30-34	5
α-helix	38-39	2
β-strand	47-52	6	3
β-strand	58-63	6	4
β-strand	69-74	6	4
β-strand	78-83	6	4
β-strand	88-94	7	4
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	165-170	6	6
β-strand	175-181	7	6
β-strand	187-192	6	7
β-strand	198-203	6	7
β-strand	207-212	6	7
β-strand	218-223	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	335-339	5	3

Chain G: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	20-23	4
α-helix	30-43	14
α-helix	53-55	3

Chain N: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	10
β-strand	10-11	2	11
β-strand	20-25	6	10
β-strand	34-40	7	11
β-strand	43-51	9	11
β-strand	59-60	2	11
α-helix	62-64	3
β-strand	69-73	5	10
β-strand	78-82	5	10
α-helix	88-90	3
β-strand	92-98	7	11
β-strand	118	1	11
β-strand	122-125	4	11

Chain R: 15 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	48	1
α-helix	49-53	5
α-helix	54-78	25
α-helix	85-112	28
α-helix	122-154	33
α-helix	158-160	3
α-helix	165-182	18
α-helix	186-189	4
β-strand	192-194	3	12
β-strand	200-202	3	12
α-helix	211-221	11
α-helix	222-227	6
α-helix	228-245	18
α-helix	255-288	34
α-helix	296-321	26
α-helix	322-326	5
α-helix	329-334	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
GNAS complex locus	A	protein	265	Homo sapiens	P63092 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	377	Homo sapiens	P62873 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	G	protein	71	Homo sapiens	P59768 (AlphaFold model)
Nanobody 35	N	protein	157	Homo sapiens
Soluble cytochrome b562,P2Y purinoceptor 1	R	protein	680	Escherichia coli, Homo sapiens	P0ABE7 (AlphaFold model), P47900, Q9GV45

Sequence of entity 1 (A), FASTA

>8WJX_1 GNAS complex locus (chains A)
MGMGHHHHHHENLYFQGNSKTEDQRNEEKAQREANKKIEKQLQKDKQVYRATHRLLLLGA
DNSGKSTIVKQMRILHGGSGGSGGTSGIFETKFQVDKVNFHMFDVGGQRDERRKWIQCFN
DVTAIIFVVDSSDYNRLQEALNLFKSIWNNRWLRTISVILFLNKQDLLAEKVLAGKSKIE
DYFPEFARYTTPEDATPEPGEDPRVTRAKYFIRDEFLRISTASGDGRHYCYPHFTCAVDT
ENARRIFNDCKDIILQMNLREYNLV

Sequence of entity 2 (B), FASTA

>8WJX_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
MHHHHHHGSLLQSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRR
TLRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSG
NYVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALW
DIETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDI
NAICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGY
DDFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWNGSSGGGGSG
GGGSSGVSGWRLFKKIS

Sequence of entity 3 (G), FASTA

>8WJX_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 4 (N), FASTA

>8WJX_4 Nanobody 35 (chains N)
MKYLLPTAAAGLLLLAAQPAMAMQVQLQESGGGLVQPGGSLRLSCAASGFTFSNYKMNWV
RQAPGKGLEWVSDISQSGASISYTGSVKGRFTISRDNAKNTLYLQMNSLKPEDTAVYYCA
RCPAPFTRDCFDVTSTTYAYRGQGTQVTVSSHHHHHH

Sequence of entity 5 (R), FASTA

>8WJX_5 Soluble cytochrome b562,P2Y purinoceptor 1 (chains R)
MKTIIALSYIFCLVFADYKDDDDAGRAHHHHHHHHHHENLYFQSGAPADLEDNWETLNDN
LKVIEKADNAAQVKDALTKMRAAALDAQKATPPKLEDKSPDSPEMKDFRHGFDILVGQID
DALKLANEGKVKEAQAAAEQLKTTRNAYIQKYLEFLEVLFQGPTEVLWPAVPNGTDAAFL
AGPGSSWGNSTVASTAAVSSSFKCALTKTGFQFYYLPAVYILVFIIGFLGNSVAIWMFVF
HMKPWSGISVYMFNLALADFLYVLTLPALIFYYFNKTDWIFGDAMCKLQRFIFHVNLYGS
ILFLTCISAHRYSGVVYPLKSLGRLKKKNAICISVLVWLIVVVAISPILFYSGTGVRKNK
TITCYDTTSDEYLRSYFIYSMCTTVAMFCVPLVLILGCYGLIVRALIYKDLDNSPLRRKS
IYLVIIVLTVFAVSYIPFHVMKTMNLRARLDFQTPAMCAFNDRVYATYQVTRGLASLNSC
VDPILYFLAGDTFRRRLSRATRKASRRSEANLQSKSEDMTLNVFTLEDFVGDWEQTAAYN
LDQVLEQGGVSSLLQNLAVSVTPIQRIVRSGENALKIDIHVIIPYEGLSADQMAQIEEVF
KVVYPVDDHHFKVILPYGTLVIDGVTPNMLNYFGRPYEGIAVFDGKKITVTGTLWNGNKI
IDERLITPDGSMLFRVTINS

Ligands and cofactors

ID	Name	Formula	Copies
CLR	Cholesterol	C27 H46 O	1
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	1

Primary citation

ADP-bound purinergic receptor 1 in complex with miniGs/q. Gu, Q.C., Tang, W.Q. To be published.

Other PDB entries of the same protein (UniProt P63092 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7BPH 1.57 Å, Crystal structure of GppNHp-bound GNAS in complex with the cyclic peptide inhibitor GN13
6AU6 1.7 Å, Crystal structure of GDP-bound human GNAS R201C mutant
8F0K 1.9 Å, Human Amylin3 Receptor in complex with Gs and Pramlintide analogue peptide San385
7E5E 1.95 Å, Crystal structure of GDP-bound GNAS in complex with the cyclic peptide inhibitor GD20
7MBX 1.95 Å, Human Cholecystokinin 1 receptor (CCK1R) Gs complex
8F0J 2.0 Å, Calcitonin Receptor in complex with Gs and Pramlintide analogue peptide San45
8F2B 2.0 Å, Amylin 3 Receptor in complex with Gs and Pramlintide analogue peptide San45
9XXT 2.0 Å, Cryo-EM structure of lysophosphatidylserine (18:0)-bound GPR174-Gs complex
6X18 2.1 Å, GLP-1 peptide hormone bound to Glucagon-Like peptide-1 (GLP-1) Receptor
6X19 2.1 Å, Non peptide agonist CHU-128, bound to Glucagon-Like peptide-1 (GLP-1) Receptor
9NTU 2.1 Å, Cryo-EM structure of BETP-GLP-1(9-36)-GLP-1R-Gs complex
7RTB 2.14 Å, Peptide-19 bound to the Glucagon-Like Peptide-1 Receptor (GLP-1R)

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