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(-) Description

Title :  CRYSTAL STRUCTURE OF BOVINE 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 :  2.38
Chains :  Asym. Unit :  A,C
Biol. Unit 1:  A,C  (2x)
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
    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 25-815
    Gene: TLR9
    Organism Common: BOVINE
    Organism Scientific: BOS TAURUS
    Organism Taxid: 9913
 
Molecule 2 - DNA (5'-D(*CP*AP*TP*GP*AP*CP*GP*TP*TP*CP*CP*T)-3')
    Chains: C
    Engineered: YES
    Organism Scientific: SYNTHETIC
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AC
Biological Unit 1 (2x): AC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3WPE)

(-) Sites  (0, 0)

(no "Site" information available for 3WPE)

(-) SS Bonds  (7, 7)

Asymmetric Unit
No.Residues
1A:34 -A:44
2A:97 -A:109
3A:177 -A:183
4A:254 -A:267
5A:257 -A:264
6A:469 -A:498
7A:762 -A:788

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Leu A:32 -Pro A:33
2Phe A:271 -Pro A:272
3Ser A:361 -Leu A:362
4Ser A:790 -Pro A:791

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3WPE)

(-) Sequences/Alignments

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:714
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......ee....eee................hhhhh.eee.......ee............eee...................ee............eee.................eee.......ee.hhhhh......eee...............ee............eee..................eee.........hhhhhh......eee.........................hhhhhh......eee.........hhhhhh......eee.......hhhhhh..........eee................hhhhhh.....eee.......ee....hhhhhhh....eee.......ee.hhhhhhh....eee.............eee.........hhhhhh......eee......................eee.....................eee...hhhhhh.......hhhhhhh....eee....................eee....hhhhhh.................eee.........hhhhhhh......eee..........hhhhhhh....eee.......ee............eee.......ee............eee.........hhhhh......eee.....ee...hhhhhhhh.......eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3wpe A  29 PAFLPCELQPHGQVDCNWLFLKSVPHFSAGAPRANVTSLSLISNRIHHLHDSDFVHLSNLRVLNLKWNCPPAGLSPMHFPCRMTIEPNTFLAVPTLEELNLSYNGITTVPALPSSLVSLSLSHTSILVLGPTHFTGLHALRFLYMDGNCYYMNPCPRALEVAPGALLGLGNLTHLSLKYNNLTEVPRRLPPSLDTLLLSYNHIVTLAPEDLANLTALRVLDVGGNCRRCDHARNPCRECPKNFPKLHPDTFSHLSRLEGLVLKDSSLYKLEKDWFRGLGRLQVLDLSENFLYDYITKTTIFNDLTQLRRLNLSFNYHKKVSFAHLHLASSFGSLVSLEKLDMHGIFFRSLTNITLQSLTRLPKLQSLHLQLNFINQAQLSIFGAFPSLLFVDLSDNRISSCNLNFTLDLSRNNLVTIQQEMFTRLSRLQCLRLSHNSISQAVNGSQFVPLTSLRVLDLSHNKLDLYHGRSFTELPQLEALDLSYNSQPFSMQGVGHNLSFVAQLPSLRYLSLAHNGIHSRVSQKLSSASLRALDFSGNSLSQMWAEGDLYLCFFKGLRNLVQLDLSENHLHTLLPRHLDNLPKSLRQLRLRDNNLAFFNWSSLTVLPRLEALDLAGNQLKALSNGSLPPGIRLQKLDVSSNSIGFVIPGFFVRATRLIELNLSANALKTVDPSWFGAGTLKILDVSANPLHCAAFVDFLLERQEAVPVTCGSPG 792
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       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     ||750       760  ||   773      |788    
                                                                                                                                                                                                                                                                                                                                                                                                                                        427|                                                                                                                                                                                                                                                                                 744|             763|          780|      
                                                                                                                                                                                                                                                                                                                                                                                                                                         468                                                                                                                                                                                                                                                                                  747              767           786      


Chain C from PDB  Type:DNA  Length:6
                                      
                 3wpe C   4 GACGTT   9
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (27, 27)

Asymmetric Unit(hide GO term definitions)

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  Sites
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  Cis Peptide Bonds
    Leu A:32 - Pro A:33   [ RasMol ]  
    Phe A:271 - Pro A:272   [ RasMol ]  
    Ser A:361 - Leu A:362   [ RasMol ]  
    Ser A:790 - Pro A:791   [ RasMol ]  
 
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 Related Entries

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(-) Related Entries Specified in the PDB File

3wpb 3wpc 3wpd 3wpf 3wpg 3wph 3wpi