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(-) Description

Title :  CRYSTAL STRUCTURE OF TLR13-SSRNA13 COMPLEX
 
Authors :  W. Song, Z. Han, J. Chai
Date :  26 Mar 15  (Deposition) - 07 Oct 15  (Release) - 28 Oct 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Immune Receptor, Toll-Like Receptor, Ssrna, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Song, J. Wang, Z. Han, Y. Zhang, H. Zhang, W. Wang, J. Chang, B. Xia, S. Fan, D. Zhang, J. Wang, H. W. Wang, J. Chai
Structural Basis For Specific Recognition Of Single-Strande Rna By Toll-Like Receptor 13
Nat. Struct. Mol. Biol. V. 22 782 2015
PubMed-ID: 26323037  |  Reference-DOI: 10.1038/NSMB.3080

(-) Compounds

Molecule 1 - TOLL-LIKE RECEPTOR 13
    Chains: A, D
    Engineered: YES
    Expression System: INSECT CELL EXPRESSION VECTOR PTIE1
    Expression System Taxid: 266783
    Fragment: UNP RESIDUES 69-777
    Gene: TLR13
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 2 - DNA (5'-R(P*AP*CP*GP*GP*AP*AP*AP*GP*AP*CP*CP*CP*C)-3')
    Chains: B, C
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 32)

Asymmetric/Biological Unit (1, 32)
No.NameCountTypeFull Name
1NAG32Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (26, 26)

Asymmetric Unit (26, 26)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELEU A:329 , GLY A:332 , HIS A:333 , ASN A:357 , SER A:382 , ASP A:383 , HOH A:1018 , HOH A:1059binding site for residue NAG A 909
02AC2SOFTWAREGLY A:619 , ASN A:644binding site for residue NAG A 914
03AC3SOFTWAREASN A:93 , GLU A:96binding site for Mono-Saccharide NAG A 915 bound to ASN A 93
04AC4SOFTWAREHIS A:83 , HIS A:107 , ASN A:109 , HOH A:1053 , A B:6binding site for Poly-Saccharide residues NAG A 901 through NAG A 902 bound to ASN A 109
05AC5SOFTWAREASN A:125binding site for Mono-Saccharide NAG A 903 bound to ASN A 125
06AC6SOFTWARETRP A:140 , LYS A:141 , ILE A:142 , SER A:165 , ASN A:167binding site for Mono-Saccharide NAG A 904 bound to ASN A 167
07AC7SOFTWAREARG A:207 , ASN A:233 , HOH A:1086binding site for Mono-Saccharide NAG A 905 bound to ASN A 233
08AC8SOFTWAREASN A:274 , LYS A:297 , SER A:298binding site for Mono-Saccharide NAG A 906 bound to ASN A 274
09AC9SOFTWAREGLU A:255 , SER A:278 , ASN A:300 , ASP A:323 , HOH A:1041 , HOH A:1054binding site for Poly-Saccharide residues NAG A 907 through NAG A 908 bound to ASN A 300
10AD1SOFTWARETYR A:386 , ASN A:388binding site for Mono-Saccharide NAG A 910 bound to ASN A 388
11AD2SOFTWAREASN A:413 , ASP A:437 , SER A:441binding site for Mono-Saccharide NAG A 911 bound to ASN A 413
12AD3SOFTWAREARG A:372 , PRO A:396 , ASN A:421 , HIS D:558 , SER D:561 , GLU D:564 , LYS D:591 , LYS D:593 , HOH D:1063binding site for Poly-Saccharide residues NAG A 912 through NAG A 913 bound to ASN A 421
13AD4SOFTWAREASN D:93 , GLU D:96 , VAL D:117 , HOH D:1001binding site for Mono-Saccharide NAG D 917 bound to ASN D 93
14AD5SOFTWAREA C:6 , HIS D:83 , ILE D:87 , HIS D:107 , ASN D:109 , HOH D:1028 , HOH D:1047 , HOH D:1076 , HOH D:1155binding site for Poly-Saccharide residues NAG D 901 through NAG D 902 bound to ASN D 109
15AD6SOFTWAREASN D:125 , HOH D:1057binding site for Mono-Saccharide NAG D 903 bound to ASN D 125
16AD7SOFTWARESER D:127 , ASN D:152binding site for Mono-Saccharide NAG D 904 bound to ASN D 152
17AD8SOFTWARETRP D:140 , LYS D:141 , ILE D:142 , SER D:165 , ASN D:167binding site for Mono-Saccharide NAG D 905 bound to ASN D 167
18AD9SOFTWAREASN D:233 , ARG D:279 , NAG D:911binding site for Poly-Saccharide residues NAG D 906 through NAG D 907 bound to ASN D 233
19AE1SOFTWAREHIS D:241 , ASN D:263 , SER D:265 , ASN D:287binding site for Mono-Saccharide NAG D 908 bound to ASN D 263
20AE2SOFTWAREASN D:274 , SER D:298 , HOH D:1002 , HOH D:1006binding site for Mono-Saccharide NAG D 909 bound to ASN D 274
21AE3SOFTWAREGLU D:255 , SER D:278 , ARG D:279 , ASN D:300 , ASP D:323 , NAG D:907 , HOH D:1003 , HOH D:1022binding site for Poly-Saccharide residues NAG D 910 through NAG D 911 bound to ASN D 300
22AE4SOFTWARELEU D:329 , ARG D:330 , GLY D:332 , HIS D:333 , ASN D:357 , HOH D:1052 , HOH D:1105binding site for Mono-Saccharide NAG D 912 bound to ASN D 357
23AE5SOFTWARETYR D:386 , ASN D:388 , ASP D:389binding site for Mono-Saccharide NAG D 913 bound to ASN D 388
24AE6SOFTWAREPRO D:224 , VAL D:247 , SER D:248 , ASN D:413 , ARG D:414 , ASP D:437 , HOH D:1017 , HOH D:1107 , HOH D:1144binding site for Mono-Saccharide NAG D 914 bound to ASN D 413
25AE7SOFTWAREARG D:372 , SER D:397 , ASN D:421binding site for Mono-Saccharide NAG D 915 bound to ASN D 421
26AE8SOFTWAREGLY D:619 , SER D:620 , ASN D:644binding site for Mono-Saccharide NAG D 916 bound to ASN D 644

(-) SS Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1A:74 -A:86
2A:340 -A:370
3A:733 -A:760
4A:735 -A:777
5D:74 -D:86
6D:340 -D:370
7D:733 -D:760
8D:735 -D:777

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4Z0C)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Z0C)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Z0C)

(-) Exons   (0, 0)

(no "Exon" information available for 4Z0C)

(-) 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:709
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee..eeeeee.......hhhhhhh.......eee.......ee............eee.......ee............eee.......ee...........eee.......ee............eee.......hhhhhhhhhh......eee.............ee.....eee........ee...ee.....eee...........ee........eee......hhhhhhhhhhh...eee....hhhhh..hhhhhhhhhh......eee......hhhhhhhhhhhh...eee........ee............eee.......ee............eee.....................eee.........hhhhhh......eee.....................eee.......ee............eee.......ee............eee.....................eee..........................eee........ee.............eee......eee............eee.....hhhhheee............eee.....................eee.....................eee........hhhhhhhhhhhhhh......hhhhh.........hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4z0c A  69 YGFNKCTQYEFDIHHVLCIRKKITNLTEAISDIPRYTTHLNLTHNEIQVLPPWSFTNLSALVDLRLEWNSIWKIDEGAFRGLENLTLLNLVENKIQSVNNSFEGLSSLKTLLLSHNQITHIHKDAFTPLIKLKYLSLSRNNISDFSGILEAVQHLPCLERLDLTNNSIMYLDHSPRSLVSLTHLSFEGNKLRELNFSALSLPNLTNLSASRNGNKVIQNVYLKTLPQLKSLNLSGTVIKLENLSAKHLQNLRAMDLSNWELRHGHLDMKTVCHLLGNLPKLETLVFQKNVTNAEGIKQLAKCTRLLFLDLGQNSDLIYLNDSEFNALPSLQKLNLNKCQLSFINNRTWSSLQNLTSLDLSHNKFKSFPDFAFSPLKHLEFLSLSRNPITELNNLAFSGLFALKELNLAACWIVTIDRYSFTQFPNLEVLDLGDNNIRTLNHGTFRPLKKLQSLILSHNCLKILEPNSFSGLTNLRSLDLMYNSLSYFHEHLFSGLEKLLILKLGFNKITYETTRTLQYPPFIKLKSLKQLNLEGQRHGIQVVPSNFFQGLGSLQELLLGKNPSVFLDHHQFDPLINLTKLDISGTKDGDRSLYLNASLFQNLKRLKILRLENNNLESLVPDMFSSLQSLQVFSLRFNNLKVINQSHLKNLKSLMFFDVYGNKLQCTCDNLWFKNWSMNTEEVHIPFLRSYPCQQPGSQSLLIDFDDAMC 777
                                    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       428       438       448       458       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       768         


Chain B from PDB  Type:RNA  Length:13
                                             
                 4z0c B   1 ACGGAAAGACCCC  13
                                    10   


Chain C from PDB  Type:RNA  Length:13
                                             
                 4z0c C   1 ACGGAAAGACCCC  13
                                    10   


Chain D from PDB  Type:PROTEIN  Length:709
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee..eeeeee.......hhhhhhh.......eee.......ee............eee.......ee............eee.......ee...........eee.......ee............eee.......hhhhhhhhhh......eee.............ee.....eee........ee...ee.....eee...........ee........eee......hhhhhhhhhh....eee....hhhhh..hhhhhhhhhh......eee......hhhhhhhhhhhh...eee........ee............eee.......ee............eee.....................eee.........hhhhhh......eee.....................eee.......ee............eee.......ee............eee.....................eee..........................eee........ee.............eee......eee............eee.....hhhhheee............eee.....................eee.....................eee........hhhhhhhhhhhhhh......hhhhh.........hhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4z0c D  69 YGFNKCTQYEFDIHHVLCIRKKITNLTEAISDIPRYTTHLNLTHNEIQVLPPWSFTNLSALVDLRLEWNSIWKIDEGAFRGLENLTLLNLVENKIQSVNNSFEGLSSLKTLLLSHNQITHIHKDAFTPLIKLKYLSLSRNNISDFSGILEAVQHLPCLERLDLTNNSIMYLDHSPRSLVSLTHLSFEGNKLRELNFSALSLPNLTNLSASRNGNKVIQNVYLKTLPQLKSLNLSGTVIKLENLSAKHLQNLRAMDLSNWELRHGHLDMKTVCHLLGNLPKLETLVFQKNVTNAEGIKQLAKCTRLLFLDLGQNSDLIYLNDSEFNALPSLQKLNLNKCQLSFINNRTWSSLQNLTSLDLSHNKFKSFPDFAFSPLKHLEFLSLSRNPITELNNLAFSGLFALKELNLAACWIVTIDRYSFTQFPNLEVLDLGDNNIRTLNHGTFRPLKKLQSLILSHNCLKILEPNSFSGLTNLRSLDLMYNSLSYFHEHLFSGLEKLLILKLGFNKITYETTRTLQYPPFIKLKSLKQLNLEGQRHGIQVVPSNFFQGLGSLQELLLGKNPSVFLDHHQFDPLINLTKLDISGTKDGDRSLYLNASLFQNLKRLKILRLENNNLESLVPDMFSSLQSLQVFSLRFNNLKVINQSHLKNLKSLMFFDVYGNKLQCTCDNLWFKNWSMNTEEVHIPFLRSYPCQQPGSQSLLIDFDDAMC 777
                                    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       428       438       448       458       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       768
   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

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(no "SCOP Domain" information available for 4Z0C)

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(no "CATH Domain" information available for 4Z0C)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Z0C)

(-) Gene Ontology  (19, 19)

Asymmetric/Biological Unit(hide GO term definitions)

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