6XBJ: Human SMO-D384R complex with Gi

Structure of human SMO-D384R complex with Gi. Determined by electron microscopy at 3.88 Å resolution. Released 30 Sept 2020.

Method: Electron microscopy
Resolution: 3.88 Å
Organisms: Homo sapiens, Mus musculus
Chains: 5
Atoms: 10,198
Mol. weight: 185.95 kDa
Ligands: CLR
Released: 30 Sept 2020

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

Secondary structure: helices and β-sheets

6XBJ contains 39 α-helices and 80 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, 9 β-strands

Element	Residues	Length	Sheet
α-helix	7-31	25
β-strand	34-40	7	9
α-helix	46-53	8
β-strand	186-190	5	9
β-strand	195-200	6	9
α-helix	208-211	4
α-helix	212-215	4
β-strand	220-224	5	9
β-strand	225-226	2	10
α-helix	227-230	4
α-helix	242-254	13
β-strand	263	1	9
β-strand	266-267	2	11
β-strand	268-269	2	10
α-helix	271-277	7
α-helix	283-285	3
α-helix	296-308	13
β-strand	321-322	2	11
α-helix	330-351	22

Chain B: 4 helices, 27 β-strands

Element	Residues	Length	Sheet
α-helix	8-23	16
α-helix	30-35	6
α-helix	38-39	2
β-strand	49-52	4	12
β-strand	58-63	6	13
β-strand	70-74	5	13
β-strand	79-82	4	13
β-strand	89-93	5	13
β-strand	111-113	3	14
β-strand	121-125	5	14
β-strand	134-139	6	14
β-strand	148-151	4	15
β-strand	156-160	5	15
β-strand	166-170	5	15
β-strand	175-180	6	15
β-strand	187-191	5	16
β-strand	200-203	4	16
β-strand	207-210	4	16
β-strand	220-223	4	16
β-strand	229-234	6	17
β-strand	240-245	6	17
β-strand	250-254	5	17
β-strand	260-264	5	17
α-helix	272	1
β-strand	273-278	6	18
β-strand	284-289	6	18
β-strand	294-298	5	18
β-strand	304-308	5	18
β-strand	315-320	6	12
β-strand	327-331	5	12
β-strand	335-339	5	12

Chain G: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	10-23	14
α-helix	27-29	3
α-helix	30-43	14

Chain R: 19 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	65-66	2	1
β-strand	71	1	2
β-strand	77	1	3
β-strand	82	1	3
β-strand	88	1	2
α-helix	99-109	11
α-helix	110-113	4
α-helix	116-129	14
β-strand	134	1	1
β-strand	139-140	2	1
α-helix	144-149	6
α-helix	156-160	5
α-helix	182-184	3
β-strand	197-199	3	4
α-helix	203-205	3
β-strand	207	1	5
β-strand	210	1	5
β-strand	213-215	3	4
β-strand	216	1	6
α-helix	224-254	31
α-helix	262-281	20
α-helix	290-293	4
β-strand	295	1	7
β-strand	300	1	6
β-strand	301	1	7
α-helix	315-344	30
α-helix	352-355	4
α-helix	357-377	21
β-strand	382	1	8
β-strand	391	1	8
α-helix	397-400	4
α-helix	401-405	5
α-helix	406-428	23
α-helix	439-493	55
α-helix	512-514	3
α-helix	515-531	17

Chain S: 3 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	19
β-strand	11-12	2	20
β-strand	17-25	9	19
β-strand	33-39	7	21
β-strand	45-51	7	21
α-helix	53-55	3
β-strand	60	1	21
β-strand	68-73	6	19
α-helix	74-76	3
β-strand	78-84	7	19
β-strand	92-99	8	21
β-strand	110-111	2	21
β-strand	115-117	3	21
β-strand	118-119	2	20
β-strand	134-136	3	22
β-strand	143-147	5	23
β-strand	154	1	24
β-strand	160	1	24
β-strand	162	1	25
β-strand	164-167	4	26
α-helix	172-173	2
β-strand	174-178	5	26
β-strand	182-183	2	26
β-strand	194-196	3	23
β-strand	199-204	6	23
β-strand	213	1	22
β-strand	214-216	3	26
β-strand	219	1	25
β-strand	226	1	25
β-strand	232-234	3	22

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

>6XBJ_1 Smoothened homolog (chains R)
MAAARPARGPELPLLGLLLLLLLGDPGRGAASSGNATGPGPRSAGGSARRSAAVTGPPPP
LSHCGRAAPCEPLRYNVCLGSVLPYGATSTLLAGDSDSQEEAHGKLVLWSGLRNAPRCWA
VIQPLLCAVYMPKCENDRVELPSRTLCQATRGPCAIVERERGWPDFLRCTPDRFPEGCTN
EVQNIKFNSSGQCEVPLVRTDNPKSWYEDVEGCGIQCQNPLFTEAEHQDMHSYIAAFGAV
TGLCTLFTLATFVADWRNSNRYPAVILFYVNACFFVGSIGWLAQFMDGARREIVCRADGT
MRLGEPTSNETLSCVIIFVIVYYALMAGVVWFVVLTYAWHTSFKALGTTYQPLSGKTSYF
HLLTWSLPFVLTVAILAVAQVDGRSVSGICFVGYKNYRYRAGFVLAPIGLVLIVGGYFLI
RGVMTLFSIKSNHPGLLSEKAASKINETMLRLGIFGFLAFGFVLITFSCHFYDFFNQAEW
ERSFRDYVLCQANVTIGLPTKQPIPDCEIKNRPSLLVEKINLFAMFGTGIAMSTWVWTKA
TLLIWRRTWCRLTGQSDDEPKRIKKSKMIAKAFSKRHELLQNPGQELSFSMHTVSHDGPV
AGLAFDLNEPSADVSSAWAQHVTKMVARRGAILPQDISVTPVATDYKDDDDK

Sequence of entity 2 (A), FASTA

>6XBJ_2 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains A)
MGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKSTIVKQMKIIHEAG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TTGIVETHFTFKDLHFKMFDVGGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEM
NRMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAA
AYIQCQFEDLNKRKDTKEIYTHFTCATDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 3 (B), FASTA

>6XBJ_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

>6XBJ_4 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 5 (S), FASTA

>6XBJ_5 scFv16 (chains S)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLELKAAAHHHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
CLR	Cholesterol	C27 H46 O	1

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
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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