6XBM: Human SMO-Gi complex with 24(S),25-EC

Structure of human SMO-Gi complex with 24(S),25-EC. Determined by electron microscopy at 3.14 Å resolution. Released 30 Sept 2020.

Method: Electron microscopy
Resolution: 3.14 Å
Organisms: Homo sapiens, Mus musculus
Chains: 5
Atoms: 9,211
Mol. weight: 186.32 kDa
Ligands: CO1
Released: 30 Sept 2020

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

Secondary structure: helices and β-sheets

6XBM contains 32 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: 10 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	7-30	24
β-strand	34-40	7	5
α-helix	46-52	7
β-strand	185-190	6	5
β-strand	195-200	6	5
α-helix	208-210	3
α-helix	212-215	4
β-strand	220-226	7	5
α-helix	227-229	3
α-helix	242-254	13
β-strand	264-269	6	5
α-helix	271-280	10
α-helix	283-285	3
α-helix	296-308	13
β-strand	319-322	4	5
α-helix	330-350	21

Chain B: 4 helices, 31 β-strands

Element	Residues	Length	Sheet
α-helix	5-24	20
α-helix	30-33	4
α-helix	38-39	2
β-strand	49-51	3	6
β-strand	58-63	6	7
β-strand	69-74	6	7
β-strand	78-83	6	7
β-strand	88-94	7	7
β-strand	102-105	4	8
β-strand	111-115	5	8
β-strand	121-125	5	8
β-strand	134-139	6	8
β-strand	146-151	6	9
β-strand	156-161	6	9
β-strand	166-170	5	9
β-strand	175-180	6	9
β-strand	187-192	6	10
β-strand	198-203	6	10
β-strand	207-212	6	10
β-strand	218-223	6	10
β-strand	229-234	6	11
β-strand	240-245	6	11
β-strand	250-254	5	11
β-strand	259-264	6	11
α-helix	272-273	2
β-strand	275-278	4	12
β-strand	284-288	5	12
β-strand	294-298	5	12
β-strand	304-308	5	12
β-strand	315-317	3	13
β-strand	320	1	14
β-strand	327	1	14
β-strand	330-331	2	13
β-strand	336-338	3	6
β-strand	339	1	14

Chain G: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	10-23	14
α-helix	30-43	14

Chain R: 13 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	199	1	1
β-strand	207	1	2
β-strand	210	1	2
β-strand	213	1	1
α-helix	224-253	30
α-helix	262-282	21
α-helix	289-294	6
β-strand	295	1	3
α-helix	300	1
β-strand	301	1	3
α-helix	302	1
α-helix	313-344	32
α-helix	357-378	22
β-strand	381-383	3	4
β-strand	390-392	3	4
α-helix	397-400	4
α-helix	401-405	5
α-helix	406-432	27
α-helix	439-495	57
α-helix	515-533	19
α-helix	534-536	3

Chain S: 3 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	15
β-strand	10-12	3	16
β-strand	17-24	8	15
α-helix	29-31	3
β-strand	33-39	7	16
β-strand	45-51	7	16
β-strand	58-60	3	16
β-strand	68-73	6	15
β-strand	78-84	7	15
β-strand	92-99	8	16
β-strand	111	1	16
β-strand	115-119	5	16
β-strand	128-129	2	17
β-strand	134-136	3	18
β-strand	143-147	5	19
β-strand	148-149	2	17
β-strand	154	1	20
β-strand	160	1	20
β-strand	162-167	6	18
β-strand	174-178	5	18
β-strand	182-183	2	18
α-helix	184	1
β-strand	191-196	6	19
β-strand	199-204	6	19
β-strand	213-219	7	18
α-helix	226-228	3
β-strand	231-234	4	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Smoothened homolog	R	protein	652	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	344	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)
scFv16	S	protein	259	Mus musculus

Sequence of entity 1 (R), FASTA

>6XBM_1 Smoothened homolog (chains R)
MAAARPARGPELPLLGLLLLLLLGDPGRGAASSGNATGPGPRSAGGSARRSAAVTGPPPP
LSHCGRAAPCEPLRYNVCLGSVLPYGATSTLLAGDSDSQEEAHGKLVLWSGLRNAPRCWA
VIQPLLCAVYMPKCENDRVELPSRTLCQATRGPCAIVERERGWPDFLRCTPDRFPEGCTN
EVQNIKFNSSGQCEVPLVRTDNPKSWYEDVEGCGIQCQNPLFTEAEHQDMHSYIAAFGAV
TGLCTLFTLATFVADWRNSNRYPAVILFYVNACFFVGSIGWLAQFMDGARREIVCRADGT
MRLGEPTSNETLSCVIIFVIVYYALMAGVVWFVVLTYAWHTSFKALGTTYQPLSGKTSYF
HLLTWSLPFVLTVAILAVAQVDGDSVSGICFVGYKNYRYRAGFVLAPIGLVLIVGGYFLI
RGVMTLFSIKSNHPGLLSEKAASKINETMLRLGIFGFLAFGFVLITFSCHFYDFFNQAEW
ERSFRDYVLCQANVTIGLPTKQPIPDCEIKNRPSLLVEKINLFAMFGTGIAMSTWVWTKA
TLLIWRRTWCRLTGQSDDEPKRIKKSKMIAKAFSKRHELLQNPGQELSFSMHTVSHDGPV
AGLAFDLNEPSADVSSAWAQHVTKMVARRGAILPQDISVTPVATDYKDDDDK

Sequence of entity 2 (A), FASTA

>6XBM_2 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains A)
MGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKSTIVKQMKIIHEAG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TTGIVETHFTFKDLHFKMFDVGGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEM
NRMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAA
AYIQCQFEDLNKRKDTKEIYTHFTCATDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 3 (B), FASTA

>6XBM_3 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
PGSSGSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLA
KIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGG
LDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQ
TTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFP
NGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNV
WDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 4 (G), FASTA

>6XBM_4 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 5 (S), FASTA

>6XBM_5 scFv16 (chains S)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLELKAAAHHHHHHHH

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	2

Primary citation

Sterols in an intramolecular channel of Smoothened mediate Hedgehog signaling. Qi, X., Friedberg, L., De Bose-Boyd, R. et al. Nat Chem Biol (2020) 16:1368-1375. DOI 10.1038/s41589-020-0646-2 · 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
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
6OT0 3.84 Å, Structure of human Smoothened-Gi complex

Browse structure collections

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