5L7D - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   STRUCTURE OF HUMAN SMOOTHENED IN COMPLEX WITH CHOLESTEROL

Authors :   E. F. X. Byrne, R. Sircar, P. S. Miller, G. Hedger, G. Luchetti, S. Nachte M. D. Tully, L. Mydock-Mcgrane, D. F. Covey, R. P. Rambo, M. S. P. Sansom S. Newstead, R. Rohatgi, C. Siebold

Date :   03 Jun 16 (Deposition) - 20 Jul 16 (Release) - 10 Aug 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.20

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   G Protein Coupled Receptor, Morphogen Signaling, Hedgehog Signaling, Cholesterol, Signaling Protein, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. F. Byrne, R. Sircar, P. S. Miller, G. Hedger, G. Luchetti, S. Nachtergaele, M. D. Tully, L. Mydock-Mcgrane, D. F. Covey, R. P. Rambo, M. S. Sansom, S. Newstead, R. Rohatgi, C. Siebold
Structural Basis Of Smoothened Regulation By Its Extracellular Domains.
Nature V. 535 517 2016
PubMed-ID: 27437577 | Reference-DOI: 10.1038/NATURE18934

Molecule 1 - SMOOTHENED HOMOLOG,SOLUBLE CYTOCHROME B562,SMOOTHENED HOMOLOG
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Cell Line	:	HEK-293S-GNTI-
	Expression System Common	:	HUMAN
	Expression System Plasmid	:	PHLSEC
	Expression System Taxid	:	9606
	Fragment	:	UNP RESIDUES 32-428,UNP RESIDUES 23-127,UNP RESIDUES 443- 555
	Gene	:	SMO, SMOH, CYBC
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS, ESCHERICHIA COLI
	Organism Taxid	:	9606, 562
	Other Details	:	HUMAN SMOOTHENED WITH AN SOLUBLE E. COLI CYTOCHROME B562 PROTEIN REPLACING SMOOTHENED RESIDUES 429 TO 445.
	Synonym	:	SMO,PROTEIN GX,CYTOCHROME B-562,SMO,PROTEIN GX

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 5)

No.	Name	Count	Type	Full Name
1	CLR	1	Ligand/Ion	CHOLESTEROL
2	NA	2	Ligand/Ion	SODIUM ION
3	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 1 (2, 3)

No.	Name	Count	Type	Full Name
1	CLR	1	Ligand/Ion	CHOLESTEROL
2	NA	-1	Ligand/Ion	SODIUM ION
3	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	CLR	-1	Ligand/Ion	CHOLESTEROL
2	NA	-1	Ligand/Ion	SODIUM ION
3	NAG	-1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:95 , LEU A:108 , TRP A:109 , GLY A:111 , LEU A:112 , ASN A:114 , ARG A:161 , VAL A:210 , ALA A:492	binding site for residue CLR A 1203
2	AC2	SOFTWARE	THR A:90 , ALA A:93 , GLY A:94 , SER A:96	binding site for residue NA A 1204
3	AC3	SOFTWARE	GLU A:305 , PRO A:306 , GLU A:310 , THR A:311 , LEU A:312	binding site for residue NA A 1205
4	AC4	SOFTWARE	ASP A:165 , LYS A:186 , ASN A:188 , GLU B:1033	binding site for Mono-Saccharide NAG A 1201 bound to ASN A 188
5	AC5	SOFTWARE	GLU A:160 , ARG A:161 , ASN A:493 , LYS B:1030	binding site for Mono-Saccharide NAG A 1202 bound to ASN A 493

Asymmetric Unit

No.	Residues
1	A:64	-	A:178
2	A:70	-	A:134
3	A:78	-	A:127
4	A:118	-	A:154
5	A:147	-	A:169
6	A:193	-	A:213
7	A:217	-	A:295
8	A:314	-	A:390
9	A:490	-	A:507
10	B:64	-	B:178
11	B:70	-	B:134
12	B:78	-	B:127
13	B:118	-	B:154
14	B:147	-	B:169
15	B:193	-	B:213
16	B:217	-	B:295
17	B:314	-	B:390
18	B:490	-	B:507

Asymmetric Unit

No.	Residues
1	Val A:195	-	Pro A:196
2	Tyr A:262	-	Pro A:263
3	Glu A:305	-	Pro A:306
4	Val B:195	-	Pro B:196
5	Tyr B:262	-	Pro B:263
6	Glu B:305	-	Pro B:306

(no "SAP(SNP)/Variant" information available for 5L7D)

(no "PROSITE Motif" information available for 5L7D)

(no "Exon" information available for 5L7D)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:588
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......eee...ee....ee..ee....ee.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eee..hhhhhhhhhh.hhhhhhhh..hhhhh............................eee.............eee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh.eee......eee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                5l7d A   58 PPPLSHCGRAAPCEPLRYNVCLGSVLPYGATSTLLAGDSDSQEEAHGKLVLWSGLRNAPRCWAVIQPLLCAVYMPKCENDRVELPSRTLCQATRGPCAIVERERGWPDFLRCTPDRFPEGCTNEVQNIKFNSSGQCEVPLVRTDNPKSWYEDVEGCGIQCQNPLFTEAEHQDMHSYIAAFGAVTGLCTLFTLATFVADWRNSNRYPAVILFYVNACFFVGSIGWLAQFMDGARREIVCRADGTMRLGEPTSNETLSCVIIFVIVYYALMAGFVWFVVLTYAWHTSFKALQPLSGKTSYFHLLTWSLPFVLTVAILAVAQVDGDSVSGICFVGYKNYRYRAGFVLAPIGLVLIVGGYFLIRGVMTLFSARRQLADLEDNWETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKATPPSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRNAYIQKYLERARSTLSKINETMLRLGIFGFLAFGFVLITFSCHFYDFFNQAEWERSFRDYVLCQANVTIGLPTKQPIPDCEIKNRPSLLVEKINLFAMFGTGIAMSTWVWTKATLLIWRRTWCRLT  553
                                    67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       351       361       371       381       391       401       411       421      1013      1023      1033      1043      1053      1071      1081      1091      1101      1111      1121      1131|      455       465       475       485       495       505       515       525       535       545        
                                                                                                                                                                                                                                                                                                                          346|                                                                          428|                                              1061|                                                         1131|                                                                                                           
                                                                                                                                                                                                                                                                                                                           351                                                                          1011                                               1070                                                           446

Chain B from PDB  Type:PROTEIN  Length:578
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eee...ee....ee..ee....ee.........hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh......eee..hhhhhhhhhh.hhhhhhhh..hhhhh...........hhhhh............eee.............eee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhh.eee......eee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5l7d B   58 PPPLSHCGRAAPCEPLRYNVCLGSVLPYGATSTLLAGDSDSQEEAHGKLVLWSGLRNAPRCWAVIQPLLCAVYMPKCENDRVELPSRTLCQATRGPCAIVERERGWPDFLRCTPDRFPEGCTNEVQNIKFNSSGQCEVPLVRTDNPKSWYEDVEGCGIQCQNPLFTEAEHQDMHSYIAAFGAVTGLCTLFTLATFVADWRNSNRYPAVILFYVNACFFVGSIGWLAQFMDGARREIVCRADGTMRLGEPTSNETLSCVIIFVIVYYALMAGFVWFVVLTYAWHTSFKALGTTYQPLSGKTSYFHLLTWSLPFVLTVAILAVAQVDGDSVSGICFVGYKNYRYRAGFVLAPIGLVLIVGGYFLIRGVMTLFSARRQLADLEDNWETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKATPPSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRNAYIQKYLERARSTLSKINETMLRLGIFGFLAFGFVLITFSCHFYDFFNQAEWERSFRDYVLCQCEIKNRPSLLVEKINLFAMFGTGIAMSTWVWTKATLLIWRRTWCR  551
                                    67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427||    1019      1029      1039      1049      1059 ||   1074      1084      1094      1104      1114      1124      |448       458       468       478       488  ||   513       523       533       543        
                                                                                                                                                                                                                                                                                                                                                                                                            428|                                              1061|                                                            1131|                                          491|                                            
                                                                                                                                                                                                                                                                                                                                                                                                            1011                                               1067                                                              446                                           507

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

(no "SCOP Domain" information available for 5L7D)

(no "CATH Domain" information available for 5L7D)

(no "Pfam Domain" information available for 5L7D)

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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	Sites
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	Cis Peptide Bonds
		Glu A:305 - Pro A:306	[ RasMol ]
		Glu B:305 - Pro B:306	[ RasMol ]
		Tyr A:262 - Pro A:263	[ RasMol ]
		Tyr B:262 - Pro B:263	[ RasMol ]
		Val A:195 - Pro A:196	[ RasMol ]
		Val B:195 - Pro B:196	[ RasMol ]

Biological Units
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		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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	SMO_HUMAN \| Q99835
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(no "Related Entries Specified in the PDB File" available for 5L7D)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 5)

Sites (5, 5)

SS Bonds (18, 18)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Gene Ontology (107, 107)

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