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(-) Description

Title :  CRYSTAL STRUCTURE OF MOUSE TLR9 (UNLIGANDED FORM)
 
Authors :  U. Ohto, T. Shimizu
Date :  11 Jan 14  (Deposition) - 11 Feb 15  (Release) - 06 May 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.96
Chains :  Asym./Biol. Unit :  A
Keywords :  Leucine Rich Repeat, Receptor, Innate Immunity, Dna Binding, Glycosylation, Dna Binding Protein (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

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 15)

Asymmetric/Biological Unit (2, 15)
No.NameCountTypeFull Name
1NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
2SO412Ligand/IonSULFATE ION

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELEU A:50 , LYS A:51 , SER A:52 , HIS A:595 , HOH A:1175BINDING SITE FOR RESIDUE SO4 A 904
02AC2SOFTWARETYR A:229 , GLY A:253 , ARG A:256 , ILE A:266BINDING SITE FOR RESIDUE SO4 A 905
03AC3SOFTWAREARG A:602BINDING SITE FOR RESIDUE SO4 A 906
04AC4SOFTWARELYS A:95 , TYR A:132 , SO4 A:912 , HOH A:1045 , HOH A:1048BINDING SITE FOR RESIDUE SO4 A 907
05AC5SOFTWAREASN A:787 , LYS A:790 , GLY A:799 , ARG A:800 , SER A:801BINDING SITE FOR RESIDUE SO4 A 908
06AC6SOFTWARESER A:72 , TRP A:96BINDING SITE FOR RESIDUE SO4 A 909
07AC7SOFTWAREHIS A:76 , SER A:109 , HIS A:111 , HOH A:1131BINDING SITE FOR RESIDUE SO4 A 910
08AC8SOFTWAREARG A:377 , ASN A:404 , ARG A:426BINDING SITE FOR RESIDUE SO4 A 911
09AC9SOFTWARELYS A:95 , ASN A:129 , SO4 A:907 , HOH A:1047BINDING SITE FOR RESIDUE SO4 A 912
10BC1SOFTWARETHR A:28 , LEU A:29 , ARG A:808BINDING SITE FOR RESIDUE SO4 A 913
11BC2SOFTWARETYR A:555 , HIS A:585 , ASP A:587BINDING SITE FOR RESIDUE SO4 A 914
12BC3SOFTWAREGLN A:270 , LYS A:271 , SER A:272 , HIS A:274BINDING SITE FOR RESIDUE SO4 A 915
13BC4SOFTWARECYS A:178 , PRO A:183 , CYS A:184 , ASN A:210BINDING SITE FOR MONO-SACCHARIDE NAG A 903 BOUND TO ASN A 210
14BC5SOFTWARESER A:301 , GLN A:305 , ASN A:332 , GLN A:689 , HOH A:1110BINDING SITE FOR MONO-SACCHARIDE NAG A 902 BOUND TO ASN A 332
15BC6SOFTWARESER A:710 , ASN A:732 , SER A:734 , HIS A:735 , ASP A:757 , HOH A:1030BINDING 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  (7, 7)

Asymmetric/Biological Unit
No.Residues
1Leu A:33 -Pro A:34
2Thr A:101 -Gly A:102
3Ala A:164 -Gly A:165
4Arg A:470 -Cys A:471
5Gln A:695 -Gly A:696
6Asn A:700 -Gly A:701
7Ser A:793 -Pro A:794

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3WPF)

(-) 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:740
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eee...eee...................eee.......ee....hhhhh...eee...............ee............eee.................eee.......eehhhhhh......eee...............ee............eee..................eee.......eehhhhh.......eee.......................ee............eee.........hhhhhh......eee.....hhhhhh............eee................hhhhhhh....eee.......ee....hhhhh......eee.......ee.hhhhhh.....eee......................eee.........hhhhhh......eee......................eee.....................eee.............hhhhhhh....eee..............ee....eee....hhhhhhh..........ee....eee.........hhhhhhh......eee.........hhhhhhhh....eee.....................eee.....................eee.........hhhhhhhhhhh..eee.....ee.....hhhhhhhhhhhhh........eee............hhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wpf A  28 TLPAFLPCELKPHGLVDCNWLFLKSVPRFASCSNITRLSLISNRIHHLHNSDFVHLSNLRQLNLKWNCPPTGLSSCHMTIEPRTFLAMRTLEELNLSYNGITTVPRLPSSLVNLSLSHTNILVLDANSLAGLYSLRVLFMDGNCYYKNPCTGAVKVTPGALLGLSQLTHLSLKYNNLTKVPRQLPPSLEYLLVSYNLIVKLGPEDLAQLTSLRVLDVGGNCRRCDHAPNPCIECGQKSLHLHPETFHHLSHLEGLVLKDSSLHTLNSSWFQGLVQLSVLDLSENFLYESITHTNAFQNLTRLRKLNLSFNYRKKVSFARLHLASSFKNLVSLQELNMNGIFFRLLNKYTLRWLADLPKLHTLHLQMNFINQAQLSIFGTFRALRFVDLSDNRISGPSTNFMDRCKNFKFTMDLSRNNLVTIKPEMFVQLSRLQCLSLSHNSIAQAVNGSQFLPLTNLQVLDLSHNKLDLYHWKSFSELPQLQALDLSYNSQPFGIGHQFSFVTHLSMLQSLSLAHNDIHTRVSSHLNSNSVRFLDFSGNGMGRMWDEGGLYLHFFQGLSGLLKLDLSQNNLHILRPQNLDNLPKSLKLLSLRDNYLSFFNWTSLSFLPNLEVLDLAGNQLKALTQGTLPNGTLLQKLDVSSNSIVSVVPAFFALAVELKEVNLSHNILKTVDRSWFGPIVMQLTVLDVRSNPLHCACGAAFVDLLLEVQTKVPGLANGVKCGSPGQLQGRSIFAQDLRLC 810
                                    37        47        60        70        80        90       100   ||  114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       467       477       487       497       507       517       527       537       547       557  ||   570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810
                                                       56|                                         104|                                                                                                                                                                                                                                                                                                                                432|                                                                                           560|                                                                                                                                                                                                                                                      
                                                        60                                          109                                                                                                                                                                                                                                                                                                                                 466                                                                                            564
   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 3WPF)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (65, 65)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ala A:164 - Gly A:165   [ RasMol ]  
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    Asn A:700 - Gly A:701   [ RasMol ]  
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    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: 3wpg 3wph 3wpi 4qdh

(-) Related Entries Specified in the PDB File

3wpb 3wpc 3wpd 3wpe 3wpg 3wph 3wpi