7ZI0: Human Smoothened

Structure of human Smoothened in complex with cholesterol and SAG. Determined by X-ray diffraction at 3.0 Å resolution. Released 15 Jun 2022.

Method: X-ray diffraction
Resolution: 3.0 Å
Organism: Homo sapiens
Chains: 2
Atoms: 9,409
Mol. weight: 143.95 kDa
Ligands: V0S, CLR, NAG, MPG
Released: 15 Jun 2022

Explore 7ZI0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7ZI0 contains 62 α-helices and 31 β-strands across 2 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: 32 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	59-61	3
α-helix	62-64	3
β-strand	65-67	3	1
β-strand	71-72	2	2
β-strand	77-78	2	3
β-strand	81-82	2	3
β-strand	87-88	2	2
α-helix	99-109	11
α-helix	110-113	4
α-helix	116-130	15
β-strand	134-135	2	1
β-strand	138-140	3	1
α-helix	141-143	3
α-helix	144-151	8
α-helix	155-160	6
α-helix	165-167	3
β-strand	197-199	3	4
α-helix	203-205	3
β-strand	213-215	3	4
β-strand	216	1	5
α-helix	224-254	31
α-helix	256-259	4
α-helix	264-282	19
α-helix	283-285	3
α-helix	289-294	6
β-strand	295	1	6
β-strand	300	1	5
β-strand	301	1	6
α-helix	302	1
β-strand	305	1	7
α-helix	313-342	30
α-helix	344-346	3
α-helix	357-378	22
β-strand	381-384	4	7
β-strand	389-392	4	7
α-helix	397-400	4
α-helix	401-405	5
α-helix	406-452	47
α-helix	456-475	20
α-helix	489-514	26
α-helix	517-530	14
α-helix	531-536	6
α-helix	537-547	11
α-helix	551-599	49
α-helix	607-610	4
α-helix	619-637	19
α-helix	638-640	3
α-helix	643-656	14

Chain B: 30 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	59-61	3
β-strand	65-67	3	8
β-strand	71-72	2	9
β-strand	77-78	2	10
β-strand	81-82	2	10
β-strand	87-88	2	9
α-helix	99-109	11
α-helix	110-113	4
α-helix	116-130	15
β-strand	134	1	8
β-strand	138-140	3	8
α-helix	141-143	3
α-helix	144-151	8
α-helix	155-160	6
α-helix	165-167	3
α-helix	189-191	3
α-helix	193-194	2
β-strand	197-199	3	11
β-strand	213-215	3	11
β-strand	216	1	12
α-helix	224-254	31
α-helix	256-259	4
α-helix	264-282	19
α-helix	283-285	3
α-helix	289-294	6
β-strand	295	1	13
β-strand	300	1	12
β-strand	301	1	13
α-helix	302	1
α-helix	313-342	30
α-helix	357-378	22
β-strand	381-384	4	14
β-strand	389-392	4	14
α-helix	397-400	4
α-helix	401-405	5
α-helix	406-452	47
α-helix	456-475	20
α-helix	489-514	26
α-helix	517-530	14
α-helix	531-536	6
α-helix	537-547	11
α-helix	551-594	44
α-helix	619-637	19
α-helix	638-640	3
α-helix	643-654	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Smoothened homolog,Soluble cytochrome b562	A, B	protein	638	Homo sapiens	P0ABE7 (AlphaFold model), Q99835 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>7ZI0_1 Smoothened homolog,Soluble cytochrome b562 (chains A, B)
SSGNATGPGPRSAGGSARRSAAVTGPPPPLSHCGRAAPCEPLRYNVCLGSVLPYGATSTL
LAGDSDSQEEAHGKLVLWSGLRNAPRCWAVIQPLLCAVYMPKCENDRVELPSRTLCQATR
GPCAIVERERGWPDFLRCTPDRFPEGCTNEVQNIKFNSSGQCEVPLVRTDNPKSWYEDVE
GCGIQCQNPLFTEAEHQDMHSYIAAFGAVTGLCTLFTLATFVADWRNSNRYPAVILFYVN
ACFFVGSIGWLAQFMDGARREIVCRADGTMRLGEPTSNETLSCVIIFVIVYYALMAGFVW
FVVLTYAWHTSFKALGTTYQPLSGKTSYFHLLTWSLPFVLTVAILAVAQVDGDSVSGICF
VGYKNYRYRAGFVLAPIGLVLIVGGYFLIRGVMTLFSARRQLADLEDNWETLNDNLKVIE
KADNAAQVKDALTKMRAAALDAQKATPPKLEDKSPDSPEMKDFRHGFDILVGQIDDALKL
ANEGKVKEAQAAAEQLKTTRNAYIQKYLERARSTLSKINETMLRLGIFGFLAFGFVLITF
SCHFYDFFNQAEWERSFRDYVLCQANVTIGLPTKQPIPDCEIKNRPSLLVEKINLFAMFG
TGIAMSTWVWTKATLLIWRRTWCRLTGQGTETSQVAPA

Ligands and cofactors

ID	Name	Formula	Copies
V0S	3-chloro-N-[trans-4-(methylamino)cyclohexyl]-N-{[3-(pyridin-4-yl)phenyl]methyl}…	C28 H28 Cl N3 O S	2
CLR	Cholesterol	C27 H46 O	2
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1
MPG	[(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate	C21 H40 O4	1

Water and common crystallization additives (NA) are not listed.

Primary citation

Patched 1 regulates Smoothened by controlling sterol binding to its extracellular cysteine-rich domain. Kinnebrew, M., Woolley, R.E., Ansell, T.B. et al. Sci Adv (2022) 8:eabm5563-eabm5563. DOI 10.1126/sciadv.abm5563 · PubMed

Other PDB entries of the same protein (UniProt P0ABE7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6DYF 1.1 Å, Cu(II)-bound structure of the engineered cyt cb562 variant, CH3Y
5YO6 1.2 Å, Crystal Structure of B562RIL with engineered disulfide bond T9C-A36C
4JEA 1.22 Å, Crystal structure of an engineered Zn-RIDC1 construct with four interfacial disulfide…
7LSJ 1.26 Å, Cu-bound crystal structure of the engineered cyt cb562 variant, DiCyt2 - H63A,…
7MK4 1.27 Å, Co-bound crystal structure of the engineered cyt cb562 variant, DiCyt2
6DYC 1.33 Å, Co(II)-bound structure of the engineered cyt cb562 variant, CH3
5YO4 1.37 Å, Crystal Structure of B562RIL with engineered disulfide bond K27C-A79C
256B 1.4 Å, Improvement of the 2.5 Å resolution model of cytochrome B562 by redetermining the…
6OT4 1.4 Å, Bimetallic dodecameric cage design 2 (BMC2) from cytochrome cb562
7LRV 1.4 Å, Ni-bound crystal structure of the engineered cyt cb562 variant, DiCyt2, crystallized in…
9PQ4 1.48 Å, Bi-bound structure of the H77C variant of TriCyt2
6DYG 1.49 Å, Fe(II)-bound structure of the engineered cyt cb562 variant, CH3Y

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