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(-) Description

Title :  CRYSTAL STRUCTURE OF MOUSE TLR9 IN COMPLEX WITH INHIBITORY DNA_SUPER
 
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

(-) 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 26-818
    Gene: TLR9
    Mutation: YES
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 2 - DNA (5'- D(*CP*CP*TP*CP*AP*AP*TP*AP*GP*GP*GP*TP*GP*AP*GP*GP*GP*G)-3')
    Chains: B
    Engineered: YES
    Organism Scientific: SYNTHETIC
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:710 , ASN A:732 , SER A:734 , ASP A:757 , HOH A:1038 , HOH A:1053BINDING SITE FOR MONO-SACCHARIDE NAG A 901 BOUND TO ASN A 732

(-) SS Bonds  (8, 8)

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:471 -A:501
7A:765 -A:791
8A:767 -A:810

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Leu A:33 -Pro A:34
2Thr A:101 -Gly A:102
3Arg A:470 -Cys A:471
4Asn A:700 -Gly A:701
5Ser A:793 -Pro A:794

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3WPI)

(-) 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:727
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eee...eee..................eee.......ee....hhhhh...eee...............ee............eee.................eee.......ee............eee...............ee............eee..................eee.......eehhhhhh......eee.......................ee............eee.........hhhhhh......eee.......hhhhh.hhhhhh....eee..........hhhhhhh....eee.......ee....hhhhh......eee.......ee.hhhhhh.....eee..................eee.........hhhhhh......eee......................eee.....................eee...........hhhhhhh....eee....................eee....hhhhhhh................eee.........hhhhhhh......eee.........hhhhhhhh....eee.....................eee.....................eee.............hhhhhhh..eee.....ee.....hhhhhhhhhhhhh........eee................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wpi A  28 TLPAFLPCELKPHGLVDCNWLFLKSVPRFSCSNITRLSLISNRIHHLHNSDFVHLSNLRQLNLKWNCPPTGLSSCHMTIEPRTFLAMRTLEELNLSYNGITTVPRLPSSLVNLSLSHTNILVLDANSLAGLYSLRVLFMDGNCYYKNPCTGAVKVTPGALLGLSQLTHLSLKYNNLTKVPRQLPPSLEYLLVSYNLIVKLGPEDLAQLTSLRVLDVGGNCRRCDHAPNPCIECGQKSLHLHPETFHHLSHLEGLVLKDSSLHTLNSSWFQGLVQLSVLDLSENFLYESITHTNAFQNLTRLRKLNLSFNYRRLHLASSFKNLVSLQELNMNGIFFRLLNKYTLRWLADLPKLHTLHLQMNFINQAQLSIFGTFRALRFVDLSDNRISGPSTMDRCKKFTMDLSRNNLVTIKPEMFVQLSRLQCLSLSHNSIAQAVNGSQFLPLTNLQVLDLSHNKLDLYHWKSFSELPQLQALDLSYNSQGIGHQFSFVTHLSMLQSLSLAHNDIHTRVSSHLNSNSVRFLDFSGNGMGRMWDEGGLYLHFFQGLSGLLKLDLSQNNLHILRPQNLDNLPKSLKLLSLRDNYLSFFNWTSLSFLPNLEVLDLAGNQLKALTQGTLPNGTLLQKLDVSSNSIVSVVPAFFALAVELKEVNLSHNILKTVDRSWFGPIVMQLTVLDVRSNPLHCACGAAFVDLLLEVQTKVPGLANGVKCGSPGQLQGRSIFAQDLRLC 810
                                    37        47        61        71        81        91       101  ||   115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345||     361       371       381       391       401       411       421       431||   ||478       488       498       508       518       528       538       548       558|      573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763       773       783       793       803       
                                                       56|                                        104|                                                                                                                                                                                                                                          346|                                                                            432| 472|                                                                                558|                                                                                                                                                                                                                                                      
                                                        61                                         109                                                                                                                                                                                                                                           353                                                                             468  475                                                                                 564                                                                                                                                                                                                                                                      


Chain B from PDB  Type:DNA  Length:9
                                         
                 3wpi B   1 CCTCGAGGG  17
                               ||    
                               4|    
                               13
   Legend:   → Mismatch (orange background)
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  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 3WPI)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (65, 65)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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 Related Entries

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

UniProtKB/Swiss-Prot
        TLR9_MOUSE | Q9EQU3: 3wpf 3wpg 3wph 4qdh

(-) Related Entries Specified in the PDB File

3wpb 3wpc 3wpd 3wpe 3wpf 3wpg 3wph