9KPD: GPCR16-miniGs complex

Cryo-EM structure of GPCR16-miniGs complex. Determined by electron microscopy at 2.84 Å resolution. Released 2 Apr 2025.

Method: Electron microscopy
Resolution: 2.84 Å
Organisms: Homo sapiens, Streptococcus pneumoniae
Chains: 5
Atoms: 8,237
Mol. weight: 207.16 kDa
Ligands: SA0
Released: 2 Apr 2025

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

Secondary structure: helices and β-sheets

9KPD contains 30 α-helices and 46 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, 7 β-strands

Element	Residues	Length	Sheet
α-helix	10-38	29
β-strand	40-47	8	1
α-helix	53-63	11
β-strand	72-79	8	1
β-strand	82-89	8	1
α-helix	100-103	4
β-strand	108-114	7	1
α-helix	121-132	12
β-strand	141-147	7	1
α-helix	149-157	9
α-helix	187-206	20
β-strand	214-215	2	1
β-strand	218	1	1
α-helix	223-246	24

Chain B: 6 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	4-25	22
α-helix	30-33	4
α-helix	38-39	2
β-strand	45-51	7	2
β-strand	58-63	6	3
β-strand	69-74	6	3
β-strand	78-83	6	3
α-helix	84-86	3
β-strand	88-94	7	3
α-helix	95	1
β-strand	100-105	6	4
β-strand	111-116	6	4
β-strand	120-125	6	4
β-strand	134-140	7	4
β-strand	146-151	6	5
β-strand	156-161	6	5
β-strand	166-170	5	5
β-strand	175-180	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	240-245	6	7
β-strand	249-254	6	7
β-strand	259-265	7	7
α-helix	272	1
β-strand	273-278	6	8
β-strand	284-289	6	8
β-strand	294-298	5	8
β-strand	304-308	5	8
β-strand	315-320	6	2
β-strand	327-331	5	2
β-strand	336-341	6	2

Chain G: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	7-23	17
α-helix	30-43	14
α-helix	53-55	3

Chain N: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	9
β-strand	11-12	2	10
β-strand	18-25	8	9
β-strand	34-39	6	11
β-strand	45-51	7	11
β-strand	58-60	3	11
α-helix	62-64	3
β-strand	68-73	6	9
β-strand	78-83	6	9
α-helix	88-90	3
β-strand	92-98	7	11
α-helix	99	1
β-strand	122-124	3	11
β-strand	125-126	2	10

Chain R: 11 helices, 0 β-strands

Element	Residues	Length
α-helix	4-38	35
α-helix	44-70	27
α-helix	82-106	25
α-helix	113-124	12
α-helix	126-140	15
α-helix	142-155	14
α-helix	174-209	36
α-helix	211-213	3
α-helix	216-248	33
α-helix	259-279	21
α-helix	281-284	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Guanine nucleotide-binding protein G(s) subunit alpha isoforms short,Guanine nucleotide-binding…	A	protein	264	Homo sapiens	P63092 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	366	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	135	Homo sapiens
Fusion protein 1,exo-alpha-sialidase,Taste receptor type 2 member 16,Fusion protein…	R	protein	1011	Homo sapiens, Streptococcus pneumoniae	Q9NYV7 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9KPD_1 Guanine nucleotide-binding protein G(s) subunit alpha isoforms short,Guanine nucleotide-binding protein G(s) subunit alpha isoforms short,Guanine nucleotide-binding protein G(t) subunit alpha-3 (chains A)
MDYKDDDDKENLYFQSNSKTEDQRNEEKAQREANKKIEKQLQKDKQVYRATHRLLLLGAD
NSGKSTIVKQMRILHGGSGGSGGTSGIFETKFQVDKVNFHMFDVGGQRDERRKWIQCFND
VTAIIFVVDSSDYNRLQEALNDFKSIWNNRWLRTISVILFLNKQDLLAEKVLAGKSKIED
YFPEFARYTTPEDATPEPGEDPRVTRAKYFIRDEFLRISTASGDGRHYCYPHFTCAVDTQ
NVKFVFDAVTDIIIKENLKDCGLF

Sequence of entity 2 (B), FASTA

>9KPD_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
MSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLAKIYA
MHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGGLDNI
CSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQTTTF
TGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFPNGNA
FATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNVWDAL
KADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWNGSSGGGGSGGGGSSGVSGWR
LFKKIS

Sequence of entity 3 (G), FASTA

>9KPD_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 4 (N), FASTA

>9KPD_4 Nanobody 35 (chains N)
MQVQLQESGGGLVQPGGSLRLSCAASGFTFSNYKMNWVRQAPGKGLEWVSDISQSGASIS
YTGSVKGRFTISRDNAKNTLYLQMNSLKPEDTAVYYCARCPAPFTRDCFDVTSTTYAYRG
QGTQVTVSSHHHHHH

Sequence of entity 5 (R), FASTA

>9KPD_5 Fusion protein 1,exo-alpha-sialidase,Taste receptor type 2 member 16,Fusion protein 2,exo-alpha-sialidase,Taste receptor type 2 member 16 (chains R)
MKTIIALSYIFCLVFADYKDDDDAHHHHHHHHHHENLYFQSAHHHHHHSSGLEVLFQGPP
EGAALTEKTDIFESGRNGNPNKDGIKSYRIPALLKTDKGTLIAGADERRLHSSDWGDIGM
VIRRSEDNGKTWGDRVTITNLRDNPKASDPSIGSPVNIDMVLVQDPETKRIFSIYDMFPE
GKGIFGMSSQKEEAYKKIDGKTYQILYREGEKGAYTIRENGTVYTPDGKATDYRVVVDPV
KPAYSDKGDLYKGDQLLGNIYFTTNKTSPFRIAKDSYLWMSYSDDDGKTWSAPQDITPMV
KADWMKFLGVGPGTGIVLRNGPHKGRILIPVYTTNNVSHLDGSQSSRVIYSDDHGKTWHA
GEAVNDNRQVDGQKIHSSTMNNRRAQNTESTVVQLNNGDVKLFMRGLTGDLQVATSKDGG
VTWEKDIKRYPQVKDVYVQMSAIHTMHEGKEYIILSNAGGPKRENGMVHLARVEENGELT
WLKHNPIQKGEFAYNSLQELGNGEYGILYEHTEKGQNAYTLSFRKFNWEFLSKNGSGSGI
PIQLTVFFMIIYVLESLTIIVQSSLIVAVLGREWLQVRRLMPVDMILISLGISRFCLQWA
SMLNNFCSYFNLNYVLCNLTITWEFFNILTFWLNSLLTVFYCIKVSSFTHHIFLWLRWRI
LRLFPWILLGCLMITCVTIIPSAIGNYIQIQLLTMEHLPRNSTVTDKLENFHQYQFQAHT
VALVIPFILFLASTIFLMASLTKQIQHHSTGHCNPSMKARFTALRSLAVLFIVFTSYFLT
ILITIIGTLFDKRCWLWVWEAFVYAFILMHSTSLMLSSPTLKRILKGKCGSGSGGSGSGG
SGSGGSGSGSSGGVFTLEDFVGDWEQTAAYNLDQVLEQGGVSSLLQNLAVSVTPIQRIVR
SGENALKIDIHVIIPYEGLSADQMAQIEEVFKVVYPVDDHHFKVILPYGTLVIDGVTPNM
LNYFGRPYEGIAVFDGKKITVTGTLWNGNKIIDERLITPDGSMLFRVTINS

Ligands and cofactors

ID	Name	Formula	Copies
SA0	2-(hydroxymethyl)phenyl beta-D-glucopyranoside	C13 H18 O7	1

Primary citation

Structural basis of beta-glucopyranoside salicin recognition by a human bitter taste GPCR. Wang, X., Zhou, C., Ao, W. et al. Cell Rep (2025) 44:115604-115604. DOI 10.1016/j.celrep.2025.115604 · PubMed

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)

Browse structure collections

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