9KPF: GPCR16-Gi complex

Cryo-EM structure of GPCR16-Gi complex. Determined by electron microscopy at 3.15 Å resolution. Released 2 Apr 2025.

Method: Electron microscopy
Resolution: 3.15 Å
Organisms: Homo sapiens, Streptococcus pneumoniae
Chains: 5
Atoms: 8,914
Mol. weight: 232.69 kDa
Ligands: SA0
Released: 2 Apr 2025

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

Secondary structure: helices and β-sheets

9KPF contains 25 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: 9 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	7-31	25
β-strand	34-40	7	1
α-helix	46-52	7
β-strand	185-191	7	1
β-strand	194-200	7	1
α-helix	209-212	4
α-helix	213-215	3
β-strand	220-226	7	1
β-strand	233	1	2
β-strand	241	1	2
α-helix	242-254	13
β-strand	263-269	7	1
α-helix	271-278	8
α-helix	283-285	3
α-helix	296-309	14
β-strand	319-323	5	1
α-helix	329-351	23

Chain B: 4 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	46-51	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	120-125	6	5
β-strand	134-140	7	5
β-strand	146-151	6	6
β-strand	156-161	6	6
β-strand	165-170	6	6
β-strand	176-181	6	6
α-helix	186	1
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	260-264	5	8
β-strand	273-278	6	9
β-strand	284-289	6	9
β-strand	293-298	6	9
β-strand	303-309	7	9
β-strand	315-320	6	3
β-strand	327-331	5	3
β-strand	335-340	6	3

Chain G: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	7-23	17
α-helix	30-43	14

Chain R: 9 helices, 0 β-strands

Element	Residues	Length
α-helix	4-39	36
α-helix	44-72	29
α-helix	83-107	25
α-helix	113-124	12
α-helix	126-155	30
α-helix	173-208	36
α-helix	219-248	30
α-helix	259-278	20
α-helix	281-286	6

Chain S: 1 helix, 25 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	10
β-strand	10-12	3	11
β-strand	17-25	9	10
β-strand	33-39	7	12
β-strand	45-51	7	12
β-strand	58-60	3	12
α-helix	62-64	3
β-strand	68-73	6	10
β-strand	78-84	7	10
β-strand	92-94	3	11
β-strand	95-99	5	12
β-strand	115-119	5	11
β-strand	129	1	13
β-strand	134-136	3	14
β-strand	143-147	5	15
β-strand	148	1	13
β-strand	154	1	16
β-strand	160	1	16
β-strand	162-167	6	14
β-strand	174-178	5	14
β-strand	182-183	2	14
β-strand	191-196	6	15
β-strand	199-204	6	15
β-strand	213-219	7	14
β-strand	227	1	14
β-strand	231-234	4	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Guanine nucleotide-binding protein G(i) subunit alpha-1	A	protein	369	Homo sapiens	P63096 (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)
Fusion protein 1,exo-alpha-sialidase,Taste receptor type 2 member 16,Fusion protein 2	R	protein	1011	Homo sapiens, Streptococcus pneumoniae	Q9NYV7 (AlphaFold model)
scFv16	S	protein	266	Homo sapiens

Sequence of entity 1 (A), FASTA

>9KPF_1 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains A)
DYKDDDDKENLYFQSMGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESG
KSTIVKQMKIIHEAGYSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDAR
QLFVLAGAAEEGFMTAELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQP
NYIPTQQDVLRTRVKTTGIVETHFTFKDLHFKMFDVGGQRSERKKWIHCFEGVTAIIFCV
ALSDYDLVLAEDEEMNRMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTI
CYPEYAGSNTYEEAAAYIQCQFEDLNKRKDTKEIYTHFTCATDTKNVQFVFDAVTDVIIK
NNLKDCGLF

Sequence of entity 2 (B), FASTA

>9KPF_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

>9KPF_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 4 (R), FASTA

>9KPF_4 Fusion protein 1,exo-alpha-sialidase,Taste receptor type 2 member 16,Fusion protein 2 (chains R)
MKTIIALSYIFCLVFADYKDDDDAHHHHHHHHHHENLYFQSAHHHHHHSSGLEVLFQGPP
EGAALTEKTDIFESGRNGNPNKDGIKSYRIPALLKTDKGTLIAGADERRLHSSDWGDIGM
VIRRSEDNGKTWGDRVTITNLRDNPKASDPSIGSPVNIDMVLVQDPETKRIFSIYDMFPE
GKGIFGMSSQKEEAYKKIDGKTYQILYREGEKGAYTIRENGTVYTPDGKATDYRVVVDPV
KPAYSDKGDLYKGDQLLGNIYFTTNKTSPFRIAKDSYLWMSYSDDDGKTWSAPQDITPMV
KADWMKFLGVGPGTGIVLRNGPHKGRILIPVYTTNNVSHLDGSQSSRVIYSDDHGKTWHA
GEAVNDNRQVDGQKIHSSTMNNRRAQNTESTVVQLNNGDVKLFMRGLTGDLQVATSKDGG
VTWEKDIKRYPQVKDVYVQMSAIHTMHEGKEYIILSNAGGPKRENGMVHLARVEENGELT
WLKHNPIQKGEFAYNSLQELGNGEYGILYEHTEKGQNAYTLSFRKFNWEFLSKNGSGSGI
PIQLTVFFMIIYVLESLTIIVQSSLIVAVLGREWLQVRRLMPVDMILISLGISRFCLQWA
SMLNNFCSYFNLNYVLCNLTITWEFFNILTFWLNSLLTVFYCIKVSSFTHHIFLWLRWRI
LRLFPWILLGCLMITCVTIIPSAIGNYIQIQLLTMEHLPRNSTVTDKLENFHQYQFQAHT
VALVIPFILFLASTIFLMASLTKQIQHHSTGHCNPSMKARFTALRSLAVLFIVFTSYFLT
ILITIIGTLFDKRCWLWVWEAFVYAFILMHSTSLMLSSPTLKRILKGKCGSGSGGSGSGG
SGSGGSGSGSSGGVFTLEDFVGDWEQTAAYNLDQVLEQGGVSSLLQNLAVSVTPIQRIVR
SGENALKIDIHVIIPYEGLSADQMAQIEEVFKVVYPVDDHHFKVILPYGTLVIDGVTPNM
LNYFGRPYEGIAVFDGKKITVTGTLWNGNKIIDERLITPDGSMLFRVTINS

Sequence of entity 5 (S), FASTA

>9KPF_5 scFv16 (chains S)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLELKAAAENLYFQSHHHHHHHH

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 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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