6KPG: CB1-G protein complex

Cryo-EM structure of CB1-G protein complex. Determined by electron microscopy at 3.0 Å resolution. Released 12 Feb 2020.

Method: Electron microscopy
Resolution: 3.0 Å
Organism: Homo sapiens
Chains: 5
Atoms: 8,805
Mol. weight: 167.22 kDa
Ligands: 8D0
Released: 12 Feb 2020

Explore 6KPG in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6KPG contains 40 α-helices and 69 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: 8 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	7-23	17
β-strand	33-35	3	1
β-strand	36-38	3	2
α-helix	46-49	4
β-strand	186-190	5	1
β-strand	195-199	5	1
β-strand	220-226	7	2
α-helix	227-230	4
β-strand	233	1	3
β-strand	241	1	3
α-helix	242-254	13
α-helix	263	1
β-strand	264-269	6	2
α-helix	271-278	8
α-helix	296-307	12
β-strand	319-324	6	2
α-helix	332-350	19

Chain B: 3 helices, 35 β-strands

Element	Residues	Length	Sheet
α-helix	4-23	20
α-helix	30-33	4
β-strand	47-51	5	4
β-strand	58-63	6	5
β-strand	69-74	6	5
β-strand	79-83	5	5
β-strand	89-92	4	5
β-strand	100	1	6
β-strand	104-105	2	7
β-strand	111-114	4	7
β-strand	116	1	6
β-strand	121-125	5	7
β-strand	134-139	6	7
β-strand	146-151	6	8
β-strand	156-161	6	8
β-strand	165	1	9
β-strand	168-170	3	8
β-strand	176-178	3	8
β-strand	181	1	9
β-strand	187-192	6	10
β-strand	198-203	6	10
β-strand	209-210	2	11
β-strand	211-212	2	10
β-strand	220-221	2	11
β-strand	229-234	6	12
β-strand	240-245	6	12
β-strand	250-252	3	13
β-strand	253-254	2	12
β-strand	262-264	3	13
β-strand	273-278	6	14
α-helix	280-282	3
β-strand	284-289	6	14
β-strand	293-298	6	14
β-strand	304	1	14
β-strand	308-309	2	14
β-strand	315-320	6	4
β-strand	327-331	5	4
β-strand	336-339	4	4

Chain C: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	9-23	15
α-helix	27-29	3
α-helix	30-33	4
α-helix	35-44	10
α-helix	45-47	3

Chain R: 20 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	115-138	24
α-helix	140-143	4
α-helix	153-162	10
α-helix	168-175	8
α-helix	190-219	30
α-helix	221-223	3
α-helix	224-227	4
α-helix	230-245	16
α-helix	250-253	4
β-strand	264	1	15
β-strand	272	1	15
α-helix	281-300	20
α-helix	302-305	4
α-helix	307-310	4
α-helix	338-349	12
α-helix	351-354	4
α-helix	356-362	7
α-helix	363-366	4
α-helix	373-380	8
α-helix	385-394	10
α-helix	395-399	5
α-helix	402-410	9

Chain S: 4 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	16
β-strand	10-12	3	17
α-helix	13	1
β-strand	17-24	8	16
α-helix	29-31	3
β-strand	33-39	7	17
β-strand	45-51	7	17
α-helix	53-55	3
β-strand	58-60	3	17
β-strand	68-73	6	16
β-strand	78-84	7	16
β-strand	92-99	8	17
β-strand	110-111	2	17
β-strand	115-119	5	17
β-strand	135-136	2	18
β-strand	143-148	6	19
β-strand	154	1	20
β-strand	160	1	20
β-strand	162-167	6	21
β-strand	174-177	4	21
β-strand	193-196	4	19
β-strand	199-204	6	19
β-strand	214-219	6	21
β-strand	227	1	21
α-helix	228-230	3
β-strand	231-232	2	21
β-strand	233-234	2	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Guanine nucleotide-binding protein G(i) subunit alpha-1	A	protein	353	Homo sapiens	P63096 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	346	Homo sapiens	P62873 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	C	protein	71	Homo sapiens	P59768 (AlphaFold model)
Cannabinoid receptor 1	R	protein	469	Homo sapiens	P21554 (AlphaFold model)
scFv16	S	protein	259	Homo sapiens

Sequence of entity 1 (A), FASTA

>6KPG_1 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains A)
GCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKSTIVKQMKIIHEAGY
SEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMTA
ELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVKT
TGIVETHFTFKDLHFKMFDVGGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMN
RMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAAA
YIQCQFEDLNKRKDTKEIYTHFTCATDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 2 (B), FASTA

>6KPG_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
IGRARGFSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGH
LAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVAC
GGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETG
QQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICF
FPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNC
NVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 3 (C), FASTA

>6KPG_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains C)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 4 (R), FASTA

>6KPG_4 Cannabinoid receptor 1 (chains R)
ADLEDNWETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKATPPKLEDKSPDSPEMKD
FRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRNAYIQKYLLEVLFQGPVPADQV
NITEFYNKSLSSFKENEENIQCGENFMDIECFMVLNPSQQLAIAVLSLTLGTFTVLENLL
VLCVILHSRSLRCRPSYHFIGSLAVADLLGSVIFVYSFIDFHVFHRKDSRNVFLFKLGGV
TASFTASVGSLFLTAIDRYISIHRPLAYKRIVTRPKAVVAFCLMWTIAIVIAVLPLLGWN
CEKLQSVCSDIFPHIDKTYLMFWIGVVSVLLLFIVYAYMYILWKAHSHAVRMIQRGTQKS
IIIHTSEDGKVQVTRPDQARMDIELAKTLVLILVVLIICWGPLLAIMVYDVFGKMNKLIK
TVFAFCSMLCLLNSTVNPIIYALRSKDLRHAFRSMFPSCEGTAQPLDNS

Sequence of entity 5 (S), FASTA

>6KPG_5 scFv16 (chains S)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLSAEDVGVYYCMQHLEYPLTFG
AGTKLELKAAAHHHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
8D0	(6~{a}~{R},9~{R},10~{a}~{R})-9-(hydroxymethyl)-3-(8-isothiocyanato-2-methyl-oct…	C26 H39 N O3 S	1

Primary citation

Activation and Signaling Mechanism Revealed by Cannabinoid Receptor-GiComplex Structures. Hua, T., Li, X., Wu, L. et al. Cell (2020) 180:655. DOI 10.1016/j.cell.2020.01.008 · 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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