5L7D: Human Smoothened

Structure of human Smoothened in complex with cholesterol. Determined by X-ray diffraction at 3.2 Å resolution. Released 20 Jul 2016.

Method: X-ray diffraction
Resolution: 3.2 Å
Organisms: Homo sapiens, Escherichia coli
Chains: 2
Atoms: 9,265
Mol. weight: 142.44 kDa
Ligands: NAG, CLR
Released: 20 Jul 2016

Explore 5L7D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5L7D contains 60 α-helices and 34 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: 30 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	59-61	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	1	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
α-helix	193-194	2
β-strand	197-199	3	4
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	256-259	4
α-helix	264-282	19
α-helix	283-285	3
α-helix	289-294	6
β-strand	295	1	7
β-strand	300	1	6
β-strand	301	1	7
β-strand	305	1	8
α-helix	313-342	30
α-helix	343-345	3
α-helix	357-378	22
β-strand	381-383	3	8
β-strand	390-392	3	8
α-helix	397-400	4
α-helix	401-405	5
α-helix	406-1034	47
α-helix	1038-1056	19
α-helix	1071-1096	26
α-helix	1099-1112	14
α-helix	1113-1117	5
α-helix	1118-1129	12
α-helix	447-493	47
α-helix	503-507	5
α-helix	515-531	17
α-helix	532-536	5
α-helix	539-552	14

Chain B: 30 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	59-61	3
β-strand	65-67	3	9
β-strand	71-72	2	10
β-strand	77-78	2	11
β-strand	81-82	2	11
β-strand	87-88	2	10
α-helix	99-109	11
α-helix	110-112	3
α-helix	116-130	15
β-strand	134	1	9
β-strand	138-140	3	9
α-helix	141-143	3
α-helix	144-151	8
α-helix	155-160	6
α-helix	165-167	3
α-helix	181-183	3
α-helix	189-191	3
α-helix	193-194	2
β-strand	197-199	3	12
β-strand	213-215	3	12
β-strand	216	1	13
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	14
β-strand	300	1	13
β-strand	301	1	14
β-strand	305	1	15
α-helix	313-342	30
α-helix	357-378	22
β-strand	381-383	3	15
β-strand	390-392	3	15
α-helix	397-400	4
α-helix	401-405	5
α-helix	406-1034	47
α-helix	1038-1057	20
α-helix	1071-1096	26
α-helix	1099-1112	14
α-helix	1113-1117	5
α-helix	1118-1129	12
α-helix	447-490	44
α-helix	515-531	17
α-helix	532-536	5
α-helix	539-550	12

Molecules and chains

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

Sequence of entity 1 (A, B), FASTA

>5L7D_1 Smoothened homolog,Soluble cytochrome b562,Smoothened homolog (chains A, B)
SSGNATGPGPRSAGGSARRSAAVTGPPPPLSHCGRAAPCEPLRYNVCLGSVLPYGATSTL
LAGDSDSQEEAHGKLVLWSGLRNAPRCWAVIQPLLCAVYMPKCENDRVELPSRTLCQATR
GPCAIVERERGWPDFLRCTPDRFPEGCTNEVQNIKFNSSGQCEVPLVRTDNPKSWYEDVE
GCGIQCQNPLFTEAEHQDMHSYIAAFGAVTGLCTLFTLATFVADWRNSNRYPAVILFYVN
ACFFVGSIGWLAQFMDGARREIVCRADGTMRLGEPTSNETLSCVIIFVIVYYALMAGFVW
FVVLTYAWHTSFKALGTTYQPLSGKTSYFHLLTWSLPFVLTVAILAVAQVDGDSVSGICF
VGYKNYRYRAGFVLAPIGLVLIVGGYFLIRGVMTLFSARRQLADLEDNWETLNDNLKVIE
KADNAAQVKDALTKMRAAALDAQKATPPKLEDKSPDSPEMKDFRHGFDILVGQIDDALKL
ANEGKVKEAQAAAEQLKTTRNAYIQKYLERARSTLSKINETMLRLGIFGFLAFGFVLITF
SCHFYDFFNQAEWERSFRDYVLCQANVTIGLPTKQPIPDCEIKNRPSLLVEKINLFAMFG
TGIAMSTWVWTKATLLIWRRTWCRLTGQGTETSQVAPA

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2
CLR	Cholesterol	C27 H46 O	1

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

Primary citation

Structural basis of Smoothened regulation by its extracellular domains. Byrne, E.F., Sircar, R., Miller, P.S. et al. Nature (2016) 535:517-522. DOI 10.1038/nature18934 · 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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