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(-) Description

Title :  CRYSTAL STRUCTURE OF HORSE TLR9 IN COMPLEX WITH AGONISTIC DNA1668_12MER
 
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 :  1.60
Chains :  Asym./Biol. Unit :  A,B,E,F
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

(-) Compounds

Molecule 1 - TOLL-LIKE RECEPTOR 9
    Chains: A, B
    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: DOMESTIC HORSE, EQUINE
    Organism Scientific: EQUUS CABALLUS
    Organism Taxid: 9796
 
Molecule 2 - DNA (5'-D(*CP*AP*TP*GP*AP*CP*GP*TP*TP*CP*CP*T)-3')
    Chains: F, E
    Engineered: YES
    Organism Scientific: SYNTHETIC
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 21)

Asymmetric/Biological Unit (4, 21)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2NA1Ligand/IonSODIUM ION
3NAG17Ligand/IonN-ACETYL-D-GLUCOSAMINE
4SO42Ligand/IonSULFATE ION

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREILE A:232 , VAL A:233 , VAL A:251 , ASN A:254 , HOH A:1028BINDING SITE FOR RESIDUE SO4 A 909
02AC2SOFTWARETHR B:598 , HOH B:1252 , HOH B:1253 , HOH B:1254 , HOH B:1255 , HOH B:1256BINDING SITE FOR RESIDUE NA B 910
03AC3SOFTWAREILE B:232 , VAL B:233 , VAL B:251 , ASN B:254 , HOH B:1023BINDING SITE FOR RESIDUE SO4 B 911
04AC4SOFTWAREPHE B:721 , ALA B:724 , LEU B:727 , ARG B:728 , LEU B:748 , SER B:751 , LEU B:752 , HOH B:1197BINDING SITE FOR RESIDUE GOL B 912
05AC5SOFTWAREHIS A:167 , ASN A:200 , HOH A:1513 , HOH A:1557 , HOH A:1761 , HOH B:1741BINDING SITE FOR MONO-SACCHARIDE NAG A 901 BOUND TO ASN A 200
06AC6SOFTWARECYS A:178 , CYS A:184 , GLY A:185 , ARG A:186 , ASN A:210 , HOH A:1058 , HOH A:1159 , HOH A:1356 , HOH A:1647BINDING SITE FOR MONO-SACCHARIDE NAG A 902 BOUND TO ASN A 210
07AC7SOFTWARESER A:217 , ALA A:241 , ASN A:242 , HOH A:1625 , HOH A:1642BINDING SITE FOR MONO-SACCHARIDE NAG A 903 BOUND TO ASN A 242
08AC8SOFTWAREGLN A:510 , ASN A:513 , SER A:515 , HOH A:1433BINDING SITE FOR MONO-SACCHARIDE NAG A 904 BOUND TO ASN A 513
09AC9SOFTWAREASN A:567 , SER A:569 , HOH A:1423 , HOH A:1730BINDING SITE FOR MONO-SACCHARIDE NAG A 905 BOUND TO ASN A 567
10BC1SOFTWARESER A:693 , ASN A:694 , PHE A:715 , HOH A:1340 , HOH A:1544 , DA F:5 , DC F:6BINDING SITE FOR MONO-SACCHARIDE NAG A 906 BOUND TO ASN A 694
11BC2SOFTWARESER A:709 , ARG A:710 , ASN A:731 , ASP A:756BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 731 RESIDUES 907 TO 908
12BC3SOFTWAREHIS B:167 , ASN B:200 , HOH B:1476BINDING SITE FOR MONO-SACCHARIDE NAG B 901 BOUND TO ASN B 200
13BC4SOFTWARECYS B:178 , CYS B:184 , GLY B:185 , ARG B:186 , ASN B:210 , HOH B:1083 , HOH B:1138 , HOH B:1224 , HOH B:1538 , HOH B:1707 , HOH B:1761BINDING SITE FOR MONO-SACCHARIDE NAG B 902 BOUND TO ASN B 210
14BC5SOFTWARESER B:217 , ASN B:242 , HOH B:1382 , HOH B:1615BINDING SITE FOR MONO-SACCHARIDE NAG B 903 BOUND TO ASN B 242
15BC6SOFTWARETHR A:598 , HOH A:1526 , HOH A:1585 , SER B:284 , ARG B:285 , GLY B:308 , ASN B:309 , HOH B:1567 , HOH B:1750 , HOH B:1779BINDING SITE FOR MONO-SACCHARIDE NAG B 904 BOUND TO ASN B 309
16BC7SOFTWARETHR B:113 , ASN B:513 , SER B:515 , HOH B:1466 , HOH B:1714 , HOH B:1715 , HOH B:1772 , HOH B:1773 , HOH B:1788BINDING SITE FOR MONO-SACCHARIDE NAG B 905 BOUND TO ASN B 513
17BC8SOFTWAREASN B:567 , SER B:569 , HOH B:1237 , HOH B:1352BINDING SITE FOR MONO-SACCHARIDE NAG B 906 BOUND TO ASN B 567
18BC9SOFTWARESER B:693 , ASN B:694 , PHE B:715 , DA E:5 , DC E:6BINDING SITE FOR MONO-SACCHARIDE NAG B 907 BOUND TO ASN B 694
19CC1SOFTWARESER B:709 , ARG B:710 , ASN B:731 , ASP B:756BINDING SITE FOR CHAIN B OF SUGAR BOUND TO ASN B 731 RESIDUES 908 TO 909

(-) SS Bonds  (14, 14)

Asymmetric/Biological Unit
No.Residues
1A:35 -A:45
2A:98 -A:110
3A:178 -A:184
4A:255 -A:268
5A:258 -A:265
6A:470 -A:500
7A:764 -A:790
8B:35 -B:45
9B:98 -B:110
10B:178 -B:184
11B:255 -B:268
12B:258 -B:265
13B:470 -B:500
14B:764 -B:790

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Leu A:33 -Pro A:34
2Phe A:272 -Pro A:273
3Ser A:792 -Pro A:793
4Leu B:33 -Pro B:34
5Phe B:272 -Pro B:273
6Ser B:792 -Pro B:793

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3WPC)

(-) Sequences/Alignments

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
(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:747
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eee...eee................hhhhh.eee.......ee............eee...................ee............eee.................eee.......ee............eee...............ee............eee..................eee.......eehhhhhh......eee......hhhhh............ee............eee.........hhhhh.......eee.......hhhhhh..........eee................hhhhhhh....eee.......ee....hhhhh......eee.......ee.hhhhh......eee.......................eee.........hhhhhh......eee......................eee.....................eee...hhhhhh.......hhhhhhh....eee..............ee....eee....hhhhhhh..........ee....eee.........hhhhhh.......eee.........hhhhhhhh....eee.......ee............eee.......ee............eee.........hhhhhh.......eee.....ee....hhhhhhhhhhhhh.hhhhhh.eeehhhhh......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wpc A  28 TLPPFLPCELQPHGLVNCNWLFLKSVPHFSAAAPRDNVTSLSLLSNRIHHLHDSDFAQLSNLQKLNLKWNCPPAGLSPMHFPCHMTIEPNTFLAVPTLEELNLSYNGITTVPALPSSLVSLILSRTNILQLDPTSLTGLHALRFLYMDGNCYYKNPCGRALEVAPGALLGLGNLTHLSLKYNNLTTVPRSLPPSLEYLLLSYNHIVTLAPEDLANLTALRVLDVGGNCRRCDHARNPCVECPHKFPQLHSDTFSHLSRLEGLVLKDSSLYQLNPRWFRGLGNLTVLDLSENFLYDCITKTKAFQGLAQLRRLNLSFNYHKKVSFAHLTLAPSFGSLLSLQELDMHGIFFRSLSQKTLQPLARLPMLQRLYLQMNFINQAQLGIFKDFPGLRYIDLSDNRISGAVEEDFMPSCKNLSFTLDLSRNNLVTVQPEMFAQLSRLQCLRLSHNSISQAVNGSQFVPLTSLQVLDLSHNKLDLYHGRSFTELPRLEALDLSYNSQPFSMRGVGHNLSFVAQLPTLRYLSLAHNGIHSRVSQQLCSTSLWALDFSGNSLSQMWAEGDLYLRFFQGLRSLIRLDLSQNRLHTLLPCTLGNLPKSLQLLRLRNNYLAFFNWSSLTLLPNLETLDLAGNQLKALSNGSLPSGTQLQRLDVSRNSIIFVVPGFFALATRLRELNLSANALRTVEPSWFGFLAGSLEVLDVSANPLHCACAAFVDFLLQVQAAVPGLPSRVKCGSPGQLQGRSIFAQDL 806
                                    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       769       779       789       799       
                                                                                                                                                                                                                                                                                                                                                                                                                                              432|                                                                                                                                                                                                                                                                                                           766|                                      
                                                                                                                                                                                                                                                                                                                                                                                                                                               464                                                                                                                                                                                                                                                                                                            768                                      


Chain B from PDB  Type:PROTEIN  Length:749
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eee...eee................hhhhh.eee.......ee............eee...................ee............eee.................eee.......ee............eee...............ee............eee..................eee.......eehhhhhh......eee......hhhhh............ee............eee..........hhhhhh.....eee.......hhhhhh..........eee................hhhhhhh....eee.......eehhhhhhhhh......eee.......ee.hhhhh......eee........................eee.........hhhhhh......eee......................eee.....................eee...hhhhhh.......hhhhhhh....eee..............ee....eee....hhhhhhh..........ee....eee.........hhhhhh.......eee.........hhhhhhhh....eee.......ee............eee.......ee............eee.........hhhhhh.......eee.....ee.....hhhhhhhhhhhhh.hhhhhh.eeehhhhh......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wpc B  28 TLPPFLPCELQPHGLVNCNWLFLKSVPHFSAAAPRDNVTSLSLLSNRIHHLHDSDFAQLSNLQKLNLKWNCPPAGLSPMHFPCHMTIEPNTFLAVPTLEELNLSYNGITTVPALPSSLVSLILSRTNILQLDPTSLTGLHALRFLYMDGNCYYKNPCGRALEVAPGALLGLGNLTHLSLKYNNLTTVPRSLPPSLEYLLLSYNHIVTLAPEDLANLTALRVLDVGGNCRRCDHARNPCVECPHKFPQLHSDTFSHLSRLEGLVLKDSSLYQLNPRWFRGLGNLTVLDLSENFLYDCITKTKAFQGLAQLRRLNLSFNYHKKVSFAHLTLAPSFGSLLSLQELDMHGIFFRSLSQKTLQPLARLPMLQRLYLQMNFINQAQLGIFKDFPGLRYIDLSDNRISGAVESEDFMPSCKNLSFTLDLSRNNLVTVQPEMFAQLSRLQCLRLSHNSISQAVNGSQFVPLTSLQVLDLSHNKLDLYHGRSFTELPRLEALDLSYNSQPFSMRGVGHNLSFVAQLPTLRYLSLAHNGIHSRVSQQLCSTSLWALDFSGNSLSQMWAEGDLYLRFFQGLRSLIRLDLSQNRLHTLLPCTLGNLPKSLQLLRLRNNYLAFFNWSSLTLLPNLETLDLAGNQLKALSNGSLPSGTQLQRLDVSRNSIIFVVPGFFALATRLRELNLSANALRTVEPSWFGFLAGSLEVLDVSANPLHCACGAAFVDFLLQVQAAVPGLPSRVKCGSPGQLQGRSIFAQDL 806
                                    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    || 467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647       657       667       677       687       697       707       717       727       737       747       757       767       777       787       797         
                                                                                                                                                                                                                                                                                                                                                                                                                                              432|                                                                                                                                                                                                                                                                                                                                                       
                                                                                                                                                                                                                                                                                                                                                                                                                                               463                                                                                                                                                                                                                                                                                                                                                       


Chain E from PDB  Type:DNA  Length:12
                                            
                 3wpc E   1 CATGACGTTCCT  12
                                    10  


Chain F from PDB  Type:DNA  Length:12
                                            
                 3wpc F   1 CATGACGTTCCT  12
                                    10
   Legend:   → Mismatch (orange background)
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  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 '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3WPC)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (39, 39)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

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        TLR9_HORSE | Q2EEY0: 3wpb 3wpd

(-) Related Entries Specified in the PDB File

3wpb 3wpd 3wpe 3wpf 3wpg 3wph 3wpi