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Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF HORSE TLR9 IN COMPLEX WITH INHIBITORY DNA4084

Authors :   U. Ohto, H. Tanji, T. Shimizu

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

Method :   X-RAY DIFFRACTION

Resolution :   2.75

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

Keywords :   Leucine Rich Repeat, Receptor, Innate Immunity, Dna Binding, Glycosylation, 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	:	UNP RESIDUES 26-817
	Gene	:	TLR9
	Organism Common	:	HORSE
	Organism Scientific	:	EQUUS CABALLUS
	Organism Taxid	:	9796

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

		1	2
Asymmetric/Biological Unit	:	A	C

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 7)

No.	Name	Count	Type	Full Name
1	NAG	4	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
2	SO4	3	Ligand/Ion	SULFATE ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:537 , GLY A:538 , ASN A:567 , NAG A:904	BINDING SITE FOR RESIDUE SO4 A 901
2	AC2	SOFTWARE	HIS A:76 , HIS A:77 , GLY A:794	BINDING SITE FOR RESIDUE SO4 A 902
3	AC3	SOFTWARE	ARG A:546	BINDING SITE FOR RESIDUE SO4 A 903
4	AC4	SOFTWARE	CYS A:178 , TYR A:179 , CYS A:184 , GLY A:185 , ASN A:210	BINDING SITE FOR MONO-SACCHARIDE NAG A 907 BOUND TO ASN A 210
5	AC5	SOFTWARE	THR A:136 , THR A:137 , GLY A:538 , ARG A:539 , ASN A:567 , SO4 A:901	BINDING SITE FOR MONO-SACCHARIDE NAG A 904 BOUND TO ASN A 567
6	AC6	SOFTWARE	SER A:709 , ARG A:710 , ASN A:731 , ASP A:756	BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 731 RESIDUES 905 TO 906

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:470	-	A:500
7	A:764	-	A:790
8	A:766	-	A:809

Asymmetric/Biological Unit

No.	Residues
1	Leu A:33	-	Pro A:34
2	Ala A:261	-	Arg A:262
3	Phe A:272	-	Pro A:273
4	Cys A:766	-	Gly A:767
5	Ser A:792	-	Pro A:793

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

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

(no "Exon" information available for 3WPD)

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:752
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eee................hhhhh.eee.......ee............eee......hhhhh........ee............eee.................eee.......ee............eee...............ee............eee..................eee.......eehhhhhh......eee.......................ee............eee.........hhhhh.......eee.......hhhhhh..........eee................hhhhhhh....eee.............hhhhh......eee.........hhhhhh......eee.......................eee..........hhhhh......eee......................eee.....................eee................hhhhh......eee....................eee....hhhhhhhh...............eee.........hhhhhhh......eee.........hhhhhhhh....eee.......ee............eee.......ee............eee.........hhhhh........eee.....ee.....hhhhhhhhhhhhh........eeehhhhh............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wpd A  28 TLPPFLPCELQPHGLVNCNWLFLKSVPHFSAAAPRDNVTSLSLLSNRIHHLHDSDFAQLSNLQKLNLKWNCPPAGLSPMHFPCHMTIEPNTFLAVPTLEELNLSYNGITTVPALPSSLVSLILSRTNILQLDPTSLTGLHALRFLYMDGNCYYKNPCGRALEVAPGALLGLGNLTHLSLKYNNLTTVPRSLPPSLEYLLLSYNHIVTLAPEDLANLTALRVLDVGGNCRRCDHARNPCVECPHKFPQLHSDTFSHLSRLEGLVLKDSSLYQLNPRWFRGLGNLTVLDLSENFLYDCITKTKAFQGLAQLRRLNLSFNYHKKVSFAHLTLAPSFGSLLSLQELDMHGIFFRSLSQKTLQPLARLPMLQRLYLQMNFINQAQLGIFKDFPGLRYIDLSDNRISGAVEEDFMPSCKNLSFTLDLSRNNLVTVQPEMFAQLSRLQCLRLSHNSISQAVNGSQFVPLTSLQVLDLSHNKLDLYHGRSFTELPRLEALDLSYNSQPFSMRGVGHNLSFVAQLPTLRYLSLAHNGIHSRVSQQLCSTSLWALDFSGNSLSQMWAEGDLYLRFFQGLRSLIRLDLSQNRLHTLLPCTLGNLPKSLQLLRLRNNYLAFFNWSSLTLLPNLETLDLAGNQLKALSNGSLPSGTQLQRLDVSRNSIIFVVPGFFALATRLRELNLSANALRTVEPSWFGFLAGSLEVLDVSANPLHCACGAAFVDFLLQVQAAVPGLPSRVKCGSPGQLQGRSIFAQDLRLCL 810
                                    37        47        57        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    || 468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       658       668       678       688       698       708       718       728       738       748       758       768       778       788       798       808  
                                                                                                                                                                                                                                                                                                                                                                                                                                              432|                                                                                                                                                                                                                                                                                                                                                          
                                                                                                                                                                                                                                                                                                                                                                                                                                               464

Chain C from PDB  Type:DNA  Length:10
                                          
                 3wpd C   1 CCTGGATGGG  10
                                    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 3WPD)

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

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

Asymmetric/Biological Unit(hide GO term definitions)

Asymmetric/Biological Unit
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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
		Ala A:261 - Arg A:262	[ RasMol ]
		Cys A:766 - Gly A:767	[ RasMol ]
		Leu A:33 - Pro A:34	[ RasMol ]
		Phe A:272 - Pro A:273	[ RasMol ]
		Ser A:792 - Pro A:793	[ RasMol ]

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	3wpd
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	TLR9_HORSE \| Q2EEY0
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	TLR9_HORSE \| Q2EEY0	:	3wpb 3wpc

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 7)

Sites (6, 6)

SS Bonds (8, 8)

Cis Peptide Bonds (5, 5)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (39, 39)

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Related Entries

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