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Asym./Biol. Unit (Jmol Viewer)

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Title :   CRYSTAL STRUCTURE OF MOUSE TLR9 IN COMPLEX WITH INHIBITORY DNA4084 (FORM 1)

Authors :   U. Ohto, T. Shimizu

Date :   11 Jan 14 (Deposition) - 11 Feb 15 (Release) - 06 May 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.25

Chains :   Asym./Biol. Unit : A,B

Keywords :   Leucine Rich Repeat, Receptor, Innate Immunity, Dna Binding, Glycosylation, Cpg Motif, Dna Binding Protein-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   U. Ohto, T. Shibata, H. Tanji, H. Ishida, E. Krayukhina, S. Uchiyama, K. Miyake, T. Shimizu
Structural Basis Of Cpg And Inhibitory Dna Recognition By Toll-Like Receptor 9
Nature V. 520 702 2015
PubMed-ID: 25686612 | Reference-DOI: 10.1038/NATURE14138

Molecule 1 - TOLL-LIKE RECEPTOR 9
	Chains	:	A
	Engineered	:	YES
	Expression System	:	DROSOPHILA MELANOGASTER
	Expression System Cell	:	SCHNEIDER 2(S2)
	Expression System Taxid	:	7227
	Expression System Vector Type	:	BACULOVIRUS
	Fragment	:	EXTRACELLULAR DOMAIN, UNP RESIDUES 26-818
	Gene	:	TLR9
	Mutation	:	YES
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

*Molecule 2 - DNA (5'-D(CPCPTPGPGPAPTPGPGPGPAPA)-3')*
	Chains	:	B
	Engineered	:	YES
	Organism Scientific	:	SYNTHETIC
	Organism Taxid	:	32630
	Synthetic	:	YES

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 6)

No.	Name	Count	Type	Full Name
1	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
2	SO4	5	Ligand/Ion	SULFATE ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:140	BINDING SITE FOR RESIDUE SO4 A 902
2	AC2	SOFTWARE	TYR A:229 , ASN A:230 , LEU A:231 , ARG A:256 , ILE A:266 , HOH A:1037	BINDING SITE FOR RESIDUE SO4 A 903
3	AC3	SOFTWARE	LEU A:50 , LYS A:51 , SER A:52 , HIS A:595 , HOH A:1010 , HOH A:1043	BINDING SITE FOR RESIDUE SO4 A 904
4	AC4	SOFTWARE	ARG A:602	BINDING SITE FOR RESIDUE SO4 A 905
5	AC5	SOFTWARE	HIS A:203 , DC B:1 , DG B:10 , DA B:11	BINDING SITE FOR RESIDUE SO4 B 101
6	AC6	SOFTWARE	SER A:710 , ASN A:732 , SER A:734 , ASP A:757	BINDING SITE FOR MONO-SACCHARIDE NAG A 901 BOUND TO ASN A 732

Asymmetric/Biological Unit

No.	Residues
1	A:35	-	A:45
2	A:98	-	A:110
3	A:178	-	A:184
4	A:255	-	A:268
5	A:258	-	A:265
6	A:471	-	A:501
7	A:765	-	A:791
8	A:767	-	A:810

Asymmetric/Biological Unit

No.	Residues
1	Leu A:33	-	Pro A:34
2	Thr A:101	-	Gly A:102
3	Arg A:470	-	Cys A:471
4	Gln A:695	-	Gly A:696
5	Asn A:700	-	Gly A:701
6	Ser A:793	-	Pro A:794

(no "SAP(SNP)/Variant" information available for 3WPG)

(no "PROSITE Motif" information available for 3WPG)

(no "Exon" information available for 3WPG)

Asymmetric/Biological 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
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Chain A from PDB  Type:PROTEIN  Length:728
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........ee..eee...................eee.......ee....hhhhh...eee.............ee...hhhhh....eee.................eee.......ee............eee...............ee............eee..................eee.......ee............eee.......................ee............eee.........hhhhh.......eee.......hhhhhh..........eee............hhhhhhh....eee.......ee....hhhhh......eee.......ee.hhhhhh.....eee....................eee.........hhhhhh......eee......................eee.....................eee...........hhhhhhh....eee..............ee....eee....hhhhhh...........ee....eee.........hhhhhhh......eee.........hhhhhhhh....eee.....................eee.....................eee.........hhhhhhhhhhh..eee.....ee.....hhhhhhhhhhhhh........eee................. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wpg A  28 TLPAFLPCELKGLVDCNWLFLKSVPRFASCSNITRLSLISNRIHHLHNSDFVHLSNLRQLNLKWNCPPTGSCHMTIEPRTFLAMRTLEELNLSYNGITTVPRLPSSLVNLSLSHTNILVLDANSLAGLYSLRVLFMDGNCYYKNPCTGAVKVTPGALLGLSQLTHLSLKYNNLTKVPRQLPPSLEYLLVSYNLIVKLGPEDLAQLTSLRVLDVGGNCRRCDHAPNPCIECGQKSLHLHPETFHHLSHLEGLVLKDSSLHTLNSSWFQGLVQLSVLDLSENFLYESITHTNAFQNLTRLRKLNLSFNYRKARLHLASSFKNLVSLQELNMNGIFFRLLNKYTLRWLADLPKLHTLHLQMNFINQAQLSIFGTFRALRFVDLSDNRISGPSTMDRCKNFKFTMDLSRNNLVTIKPEMFVQLSRLQCLSLSHNSIAQAVNGSQFLPLTNLQVLDLSHNKLDLYHWKSFSELPQLQALDLSYNSQGIGHQFSFVTHLSMLQSLSLAHNDIHTRVSSHLNSNSVRFLDFSGNGMGRMWDEGGLYLHFFQGLSGLLKLDLSQNNLHILRPQNLDNLPKSLKLLSLRDNYLSFFNWTSLSFLPNLEVLDLAGNQLKALTQGTLPNGTLLQKLDVSSNSIVSVVPAFFALAVELKEVNLSHNILKTVDRSWFGPIVMQLTVLDVRSNPLHCACGAAFVDLLLEVQTKVPGLANGVKCGSPGQLQGRSIFAQDLRLC 810
                                    37||      49      ||62        72        82        92       102|      118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       352       362       372       382       392       402       412       422       432|      477       487       497       507       517       527       537       547       557||     572       582       592       602       612       622       632       642       652       662       672       682       692       702       712       722       732       742       752       762       772       782       792       802        
                                     38|             56|                                       102|                                                                                                                                                                                                                                           347|                                                                             432|                                                                                       558|                                                                                                                                                                                                                                                      
                                      41              60                                        109                                                                                                                                                                                                                                            352                                                                              468                                                                                        564

Chain B from PDB  Type:DNA  Length:11
                                           
                 3wpg B   1 CCTGGATGGGA  11
                                    10

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 3WPG)

(no "CATH Domain" information available for 3WPG)

(no "Pfam Domain" information available for 3WPG)

Asymmetric/Biological Unit(hide GO term definitions)

Asymmetric/Biological Unit
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	Sites
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		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Arg A:470 - Cys A:471	[ RasMol ]
		Asn A:700 - Gly A:701	[ RasMol ]
		Gln A:695 - Gly A:696	[ RasMol ]
		Leu A:33 - Pro A:34	[ RasMol ]
		Ser A:793 - Pro A:794	[ RasMol ]
		Thr A:101 - Gly A:102	[ RasMol ]

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	3wpg
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	TLR9_MOUSE \| Q9EQU3
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	TLR9_MOUSE \| Q9EQU3	:	3wpf 3wph 3wpi 4qdh

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 6)

Sites (6, 6)

SS Bonds (8, 8)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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Gene Ontology (65, 65)

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