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(-) Description

Title :  CRYSTAL STRUCTURE OF MOUSE TLR9 IN COMPLEX WITH INHIBITORY DNA4084 (FORM 2)
 
Authors :  U. Ohto, T. Shimizu
Date :  11 Jan 14  (Deposition) - 11 Feb 15  (Release) - 06 May 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.33
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*GP*GP*AP*TP*GP*GP*GP*AP*A)-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  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
2SO43Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:140 , ARG A:498 , HOH A:1116BINDING SITE FOR RESIDUE SO4 A 903
2AC2SOFTWAREARG A:256 , CYS A:265 , ILE A:266 , HOH A:1057BINDING SITE FOR RESIDUE SO4 A 904
3AC3SOFTWAREHIS A:203 , TYR A:224 , LEU A:226 , DC B:1 , DG B:9 , DG B:10 , DA B:11BINDING SITE FOR RESIDUE SO4 B 101
4AC4SOFTWARESER A:301 , ASN A:328 , GLN A:331 , ASN A:332 , GLN A:689BINDING SITE FOR MONO-SACCHARIDE NAG A 902 BOUND TO ASN A 332
5AC5SOFTWARESER A:710 , ASN A:732 , SER A:734 , ASP A:757 , HOH A:1032BINDING 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 3WPH)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3WPH)

(-) 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:725
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               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.......eehhhhhh......eee.......................ee............eee.........hhhhhh......eee.....hhhhhhhh..........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.........hhhhhhhhhhh..eee.....ee.....hhhhhhhhhhhhh.hhhhhh.eee................. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wph A  28 TLPAFLPCELKGLVDCNWLFLKSVPRFASCSNITRLSLISNRIHHLHNSDFVHLSNLRQLNLKWNCPPTGSCHMTIEPRTFLAMRTLEELNLSYNGITTVPRLPSSLVNLSLSHTNILVLDANSLAGLYSLRVLFMDGNCYYKNPCTGAVKVTPGALLGLSQLTHLSLKYNNLTKVPRQLPPSLEYLLVSYNLIVKLGPEDLAQLTSLRVLDVGGNCRRCDHAPNPCIECGQKSLHLHPETFHHLSHLEGLVLKDSSLHTLNSSWFQGLVQLSVLDLSENFLYESITHTNAFQNLTRLRKLNLSFNYARLHLASSFKNLVSLQELNMNGIFFRLLNKYTLRWLADLPKLHTLHLQMNFINQAQLSIFGTFRALRFVDLSDNRISGPSTMDRCKNFKFTMDLSRNNLVTIKPEMFVQLSRLQCLSLSHNSIAQAVNGSQFLPLTNLQVLDLSHNKLDLYHWKSFSELPQLQALDLSYNSGIGHQFSFVTHLSMLQSLSLAHNDIHTRVSSHLNSNSVRFLDFSGNGMGRMWDEGGLYLHFFQGLSGLLKLDLSQNNLHILRPQNLDNLPKSLKLLSLRDNYLSFFNWTSLSFLPNLEVLDLAGNQLKALTQGTLPNGTLLQKLDVSSNSIVSVVPAFFALAVELKEVNLSHNILKTVDRSWFGPIVMQLTVLDVRSNPLHCACGAAFVDLLLEVQTKVPGLANGVKCGSPGQLQGRSIFAQDLRLC 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      |354       364       374       384       394       404       414       424       469       479       489       499       509       519       529       539       549       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765       775       785       795       805     
                                     38|             56|                                       102|                                                                                                                                                                                                                                         345|                                                                             432|                                                                                      557|                                                                                                                                                                                                                                                      
                                      41              60                                        109                                                                                                                                                                                                                                          352                                                                              468                                                                                       564                                                                                                                                                                                                                                                      


Chain B from PDB  Type:DNA  Length:12
                                            
                 3wph B   1 CCTGGATGGGAA  12
                                    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 '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (65, 65)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Arg A:470 - Cys A:471   [ RasMol ]  
    Asn A:700 - Gly A:701   [ 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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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

3wpb 3wpc 3wpd 3wpe 3wpf 3wpg 3wpi