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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN TLR8 IN COMPLEX WITH URIDINE MONONUCLEOSIDE
 
Authors :  H. Tanji, U. Ohto, T. Shimizu
Date :  30 Jul 14  (Deposition) - 14 Jan 15  (Release) - 18 Feb 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Leucine Rich Repeat, Glycosylation, Innate Immunity, Rna Recognition, Ssrna, Rna Receptor, Rna Binding, Antiviral Binding, Antitumor Drug Binding, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Tanji, U. Ohto, T. Shibata, M. Taoka, Y. Yamauchi, T. Isobe, K. Miyake, T. Shimizu
Toll-Like Receptor 8 Senses Degradation Products Of Single-Stranded Rna.
Nat. Struct. Mol. Biol. V. 22 109 2015
PubMed-ID: 25599397  |  Reference-DOI: 10.1038/NSMB.2943

(-) Compounds

Molecule 1 - TOLL-LIKE RECEPTOR 8
    ChainsA
    EngineeredYES
    Expression SystemDROSOPHILA MELANOGASTER
    Expression System Cell LineSCHNEIDER 2(S2) CELLS
    Expression System Taxid7227
    Expression System Vector TypeBACULOVIRUS
    FragmentEXTRACELLULAR DOMAIN
    GeneTLR8, UNQ249/PRO286
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 18)

Asymmetric Unit (4, 18)
No.NameCountTypeFull Name
1BMA2Ligand/IonBETA-D-MANNOSE
2MAN2Ligand/IonALPHA-D-MANNOSE
3NAG13Ligand/IonN-ACETYL-D-GLUCOSAMINE
4URI1Ligand/IonURIDINE
Biological Unit 1 (4, 36)
No.NameCountTypeFull Name
1BMA4Ligand/IonBETA-D-MANNOSE
2MAN4Ligand/IonALPHA-D-MANNOSE
3NAG26Ligand/IonN-ACETYL-D-GLUCOSAMINE
4URI2Ligand/IonURIDINE

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:348 , LYS A:350 , GLY A:351 , VAL A:378 , PHE A:405 , ARG A:429 , ASP A:543 , ASP A:545 , VAL A:573 , THR A:574 , HOH A:1042 , HOH A:1085 , HOH A:1170BINDING SITE FOR RESIDUE URI A 901
02AC2SOFTWAREASN A:80 , GLU A:81 , GLN A:84 , GLN A:519 , SER A:522 , THR A:524 , GLU A:525 , NAG A:913 , HOH A:1238BINDING SITE FOR MONO-SACCHARIDE NAG A 902 BOUND TO ASN A 80
03AC3SOFTWAREASN A:115 , GLU A:381 , GLN A:408BINDING SITE FOR MONO-SACCHARIDE NAG A 903 BOUND TO ASN A 115
04AC4SOFTWAREGLN A:139 , ASN A:160 , THR A:162 , GLU A:164 , GLU A:193BINDING SITE FOR MONO-SACCHARIDE NAG A 904 BOUND TO ASN A 160
05AC5SOFTWARESER A:222 , ARG A:225 , ILE A:246 , ASN A:247 , GLU A:691BINDING SITE FOR MONO-SACCHARIDE NAG A 905 BOUND TO ASN A 247
06AC6SOFTWARELYS A:226 , SER A:230 , LEU A:250 , ASP A:252 , SER A:254 , TYR A:291 , ASN A:293 , ASP A:462 , HIS A:464 , SER A:465 , ASN A:466 , PHE A:467 , HOH A:1074 , HOH A:1142 , HOH A:1320BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 293 RESIDUES 906 TO 910
07AC7SOFTWARELYS A:476 , CYS A:479 , SER A:489 , LEU A:490 , ASN A:511 , TYR A:534 , ASP A:536 , ARG A:569 , HOH A:1091 , HOH A:1114 , HOH A:1231BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 511 RESIDUES 911 TO 912
08AC8SOFTWAREGLU A:81 , GLN A:84 , SER A:522 , ASN A:546 , SER A:548 , NAG A:902 , HOH A:1222BINDING SITE FOR MONO-SACCHARIDE NAG A 913 BOUND TO ASN A 546
09AC9SOFTWARELYS A:476 , GLN A:478 , TYR A:534 , ASP A:560 , SER A:562 , VAL A:588 , ASN A:590 , GLU A:612 , HOH A:1047 , HOH A:1105 , HOH A:1115 , HOH A:1128 , HOH A:1213BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 590 RESIDUES 914 TO 916
10BC1SOFTWARETHR A:149 , ASN A:171 , ASN A:202 , LYS A:587 , SER A:609 , VAL A:611 , ASN A:640 , HOH A:1048 , HOH A:1053 , HOH A:1152BINDING SITE FOR MONO-SACCHARIDE NAG A 917 BOUND TO ASN A 640
11BC2SOFTWAREASN A:656 , PHE A:678 , ASN A:680 , LEU A:683 , HOH A:1046BINDING SITE FOR MONO-SACCHARIDE NAG A 918 BOUND TO ASN A 680

(-) SS Bonds  (6, 6)

Asymmetric Unit
No.Residues
1A:36 -A:49
2A:181 -A:187
3A:257 -A:270
4A:260 -A:267
5A:479 -A:509
6A:776 -A:803

(-) Cis Peptide Bonds  (7, 7)

Asymmetric Unit
No.Residues
1Tyr A:34 -Pro A:35
2Gln A:41 -Asn A:42
3Gln A:84 -Gly A:85
4Asn A:97 -Pro A:98
5Ile A:780 -Gly A:781
6Ser A:805 -Pro A:806
7Ile A:814 -Val A:815

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4R0A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4R0A)

(-) Exons   (0, 0)

(no "Exon" information available for 4R0A)

(-) 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:748
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eee..................eee.......ee............eee.........ee............eee..................eee.......eehhhhhh......eee..............ee............eee..................eee.......ee............eee.................hhhhh..ee............eee.........hhhhhh......eee.....hhhhhhhhhhhhhh....eee................hhhhhhh....eee.......eehhhhhhhhh......eee.......ee.hhhhhhh....eee.........................hhhhhh...eee.....................eee......................eee.....................eee...hhhhhh.......hhhhhhh....eee...............ee....eee....hhhhhh............ee....eee.........hhhhhhh......eee.........hhhhhhhh....eee...........hhhhh.....eee.....................eee.......................eee............hhhhhhhhhh......hhhhh................ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4r0a A  32 RSYPCDEKKQNDSVIAECSNRRLQEVPQTVGKYVTELDLSDNFITHITNESFQGLQNLTKINLNHNPNVGLNITDGAFLNLKNLRELLLEDNQLPQIPSGLPESLTELSLIQNNIYNITKEGISRLINLKNLYLAWNCYFNKVCEKTNIEDGVFETLTNLELLSLSFNSLSHVPPKLPSSLRKLFLSNTQIKYISEEDFKGLINLTLLDLSGNCPRCFNAPFPCVPCDGGASINIDRFAFQNLTQLRYLNLSSTSLRKINAAWFKNMPHLKVLDLEFNYLVGEIASGAFLTMLPRLEILDLSFNYIKGSYPQHINISRNFSKLLSLRALHLRGYVFQELREDDFQPLMQLPNLSTINLGINFIKQIDFKLFQNFSNLEIIYLSENRISPLEFDPHSNFYHFTRPLIKPQCAAYGKALDLSLNSIFFIGPNQFENLPDIACLNLSANSNAQVLSGTEFSAIPHVKYLDLTNNRLDFDNASALTELSDLEVLDLSYNSHYFRIAGVTHHLEFIQNFTNLKVLNLSHNNIYTLTDKYNLESKSLVELVFSGNRLDILWNDDDNRYISIFKGLKNLTRLDLSLNRLKHIPNEAFLNLPASLTELHINDNMLKFFNWTLLQQFPRLELLDLRGNKLLFLTDSLSDFTSSLRTLLLSHNRISHLPSGFLSEVSSLKHLDLSSNLLKTINKSALETKTTTKLSMLELHGNPFECTCDIGDFRRWMDEHLNVKIPRLVDVICASPGDQRGKSIVSL 817
                                    41        51        61        71        81        91       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433|      469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669       679       689       699       709       719       729       739       749       759       769       779       789       799       809        
                                                                                              100|                                                                                                                                                                                                                                                                                                                             433|                                                                                                                                                                                                                                                                                                                                                                     
                                                                                               113                                                                                                                                                                                                                                                                                                                              460                                                                                                                                                                                                                                                                                                                                                                     

   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 4R0A)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4R0A)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4R0A)

(-) Gene Ontology  (33, 33)

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 Related Entries

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

UniProtKB/Swiss-Prot
        TLR8_HUMAN | Q9NR973w3g 3w3j 3w3k 3w3l 3w3m 3w3n 3wn4 4qbz 4qc0 4r07 4r08 4r09 4r6a 5awa 5awb 5awc 5awd 5az5 5hdh

(-) Related Entries Specified in the PDB File

4r07 4r08 4r09