6OT0: Human Smoothened-Gi complex

Structure of human Smoothened-Gi complex. Determined by electron microscopy at 3.84 Å resolution. Released 12 Jun 2019.

Method: Electron microscopy
Resolution: 3.84 Å
Organisms: Homo sapiens, Mus musculus
Chains: 6
Atoms: 10,572
Mol. weight: 198.58 kDa
Ligands: CO1
Released: 12 Jun 2019

Explore 6OT0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6OT0 contains 40 α-helices and 69 β-strands across 6 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: 17 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	4-24	21
α-helix	27-30	4
β-strand	33-40	8	4
α-helix	43-53	11
α-helix	66-90	25
α-helix	101-111	11
α-helix	119-120	2
α-helix	121-130	10
α-helix	135-140	6
α-helix	142-145	4
α-helix	152-157	6
α-helix	159-163	5
α-helix	171-177	7
β-strand	187-191	5	4
β-strand	194-198	5	4
α-helix	211-214	4
β-strand	220-225	6	4
β-strand	233	1	5
β-strand	241	1	5
α-helix	242-254	13
β-strand	263-268	6	4
α-helix	274-280	7
α-helix	296-308	13
β-strand	320	1	4
α-helix	329-351	23

Chain B: 7 helices, 31 β-strands

Element	Residues	Length	Sheet
α-helix	3-24	22
α-helix	30-33	4
α-helix	37-39	3
β-strand	47-51	5	6
β-strand	60-63	4	7
β-strand	69-73	5	7
β-strand	78-83	6	7
β-strand	89-94	6	7
β-strand	100-105	6	8
β-strand	111-116	6	8
β-strand	120-125	6	8
β-strand	134-140	7	8
α-helix	145-146	2
β-strand	149-151	3	9
β-strand	156-160	5	9
β-strand	165-170	6	9
β-strand	175-181	7	9
α-helix	186	1
β-strand	187-192	6	10
β-strand	198-203	6	10
β-strand	208-212	5	10
β-strand	218-222	5	10
β-strand	229	1	11
β-strand	233-234	2	12
β-strand	240-242	3	12
β-strand	245	1	11
β-strand	251-254	4	12
β-strand	259-263	5	12
α-helix	271-272	2
β-strand	273	1	13
β-strand	277	1	14
β-strand	284-288	5	14
β-strand	289	1	13
β-strand	294-298	5	14
α-helix	314	1
β-strand	315-320	6	6
β-strand	327-331	5	6
β-strand	336-339	4	6

Chain G: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	6-21	16
α-helix	30-42	13

Chain H: 1 helix, 13 β-strands

Element	Residues	Length	Sheet
β-strand	7-10	4	18
β-strand	13-14	2	19
β-strand	17	1	20
β-strand	19	1	20
β-strand	22-27	6	18
β-strand	36-42	7	19
β-strand	48-55	8	19
β-strand	62-63	2	19
β-strand	71-75	5	18
β-strand	81-86	6	18
α-helix	91-93	3
β-strand	95-102	8	19
β-strand	121	1	19
β-strand	125-128	4	19

Chain L: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	7-9	3	15
β-strand	20-26	7	15
β-strand	34-39	6	16
α-helix	44	1
β-strand	45-50	6	16
β-strand	54-55	2	16
α-helix	56	1
β-strand	57	1	17
β-strand	59	1	17
β-strand	63-68	6	15
β-strand	71-76	6	15
β-strand	86-91	6	16
β-strand	103-104	2	16

Chain R: 11 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	197-199	3	1
β-strand	213-215	3	1
α-helix	224-254	31
α-helix	264-272	9
α-helix	275-280	6
β-strand	295	1	2
β-strand	301	1	2
α-helix	302	1
α-helix	306-308	3
α-helix	315-344	30
α-helix	357-375	19
β-strand	383	1	3
β-strand	390	1	3
α-helix	398-425	28
α-helix	439-493	55
α-helix	518-531	14
α-helix	541-550	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Smoothened homolog	R	protein	563	Homo sapiens	Q99835 (AlphaFold model)
Guanine nucleotide-binding protein G(i) subunit alpha-1	A	protein	354	Homo sapiens	P63096 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	351	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)
Fab light chain	L	protein	215	Mus musculus
Fab heavy chain	H	protein	239	Mus musculus

Sequence of entity 1 (R), FASTA

>6OT0_1 Smoothened homolog (chains R)
MAAARPARGPELPLLGLLLLLLLGDPGRGAASSGNATGPGPRSAGGSARRSAAVTGPPPP
LSHCGRAAPCEPLRYNVCLGSVLPYGATSTLLAGDSDSQEEAHGKLVLWSGLRNAPRCWA
VIQPLLCAVYMPKCENDRVELPSRTLCQATRGPCAIVERERGWPDFLRCTPDRFPEGCTN
EVQNIKFNSSGQCEVPLVRTDNPKSWYEDVEGCGIQCQNPLFTEAEHQDMHSYIAAFGAV
TGLCTLFTLATFVADWRNSNRYPAVILFYVNACFFVGSIGWLAQFMDGARREIVCRADGT
MRLGEPTSNETLSCVIIFVIVYYALMAGVVWFVVLTYAWHTSFKALGTTYQPLSGKTSYF
HLLTWSLPFVLTVAILAVAQVDGDSVSGICFVGYKNYRYRAGFVLAPIGLVLIVGGYFLI
RGVMTLFSIKSNHPGLLSEKAASKINETMLRLGIFGFLAFGFVLITFSCHFYDFFNQAEW
ERSFRDYVLCQANVTIGLPTKQPIPDCEIKNRPSLLVEKINLFAMFGTGIAMSTWVWTKA
TLLIWRRTWCRLTGQDYKDDDDK

Sequence of entity 2 (A), FASTA

>6OT0_2 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains A)
MGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKNTIVKQMKIIHEAG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TTGIVETHFTFKDLHFKMFDVGAQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEM
NRMHASMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAA
AYIQCQFEDLNKRKDTKEIYTHFTCSTDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 3 (B), FASTA

>6OT0_3 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
MHHHHHHGSLLQSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRR
TLRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSG
NYVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALW
DIETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDI
NAICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGY
DDFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 4 (G), FASTA

>6OT0_4 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 5 (L), FASTA

>6OT0_5 Fab light chain (chains L)
SDIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVP
SRFSGSRSGTDFTLTISSLQPEDFATYYCQQSSSSLITFGQGTKVEIKRTVAAPSVFIFP
PSDSQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 6 (H), FASTA

>6OT0_6 Fab heavy chain (chains H)
EISEVQLVESGGGLVQPGGSLRLSCAASGFNFYYSSIHWVRQAPGKGLEWVASIYSYSGS
TSYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARYPWYWWMEKPYLSLYGMDY
WGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSG
VHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHT

Ligands and cofactors

ID	Name	Formula	Copies
CO1	17-[3-(3,3-dimethyl-oxiranyl)-1-methyl-propyl]-10,13-dimethyl-2,3,4,7,8,9,10,11…	C27 H44 O2	1

Primary citation

Cryo-EM structure of oxysterol-bound human Smoothened coupled to a heterotrimeric Gi. Qi, X., Liu, H., Thompson, B. et al. Nature (2019) 571:279-283. DOI 10.1038/s41586-019-1286-0 · PubMed

Other PDB entries of the same protein (UniProt Q99835 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4JKV 2.45 Å, Structure of the human smoothened 7TM receptor in complex with an antitumor agent
4QIN 2.6 Å, Structure of the human smoothened receptor in complex with SAG1.5
4QIM 2.61 Å, Structure of the human smoothened receptor in complex with ANTA XV
4N4W 2.8 Å, Structure of the human smoothened receptor in complex with SANT-1.
5V56 2.9 Å, 2.9A XFEL structure of the multi-domain human smoothened receptor (with E194M mutation)…
5V57 3.0 Å, 3.0A SYN structure of the multi-domain human smoothened receptor in complex with TC114
7ZI0 3.0 Å, Structure of human Smoothened in complex with cholesterol and SAG
6XBM 3.14 Å, Structure of human SMO-Gi complex with 24(S),25-EC
5L7D 3.2 Å, Structure of human Smoothened in complex with cholesterol
4O9R 3.2 Å, Human Smoothened Receptor structure in complex with cyclopamine
6XBK 3.24 Å, Structure of human SMO-G111C/I496C complex with Gi
5L7I 3.3 Å, Structure of human Smoothened in complex with Vismodegib

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