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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN TLR8 IN COMPLEX WITH HYBRID-2
 
Authors :  H. Tanji, U. Ohto, T. Shimizu
Date :  22 Aug 14  (Deposition) - 26 Aug 15  (Release) - 26 Aug 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Rna Recognition, Ssrna, Leucine Rich Repeat, Rna Receptor, Innate Immunity, Glycosylation, Secreted, Structure-Based Ligand Design, Vaccine Adjuvants, Antiviral And Antitumor Drug Binding, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Ganapathi, S. V. Haren, D. J. Dowling, I. Bergelson, N. M. Shukla, S. S. Malladi, R. Balakrishna, H. Tanji, U. Ohto, T. Shimizu, S. A. David, O. Levy
Hybrid-2: Animidazoquinoline Dual Toll-Like Receptor 7/8 Agonist That Potently Activates Cytokine Production By Huma Newborn And Adult Leukocytes
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - TOLL-LIKE RECEPTOR 8
    Chains: A, B
    Engineered: YES
    Expression System: DROSOPHILA MELANOGASTER
    Expression System Cell: S2 CELL
    Expression System Taxid: 7227
    Fragment: UNP RESIDUES 27-827
    Gene: TLR8, UNQ249/PRO286
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 32)

Asymmetric/Biological Unit (4, 32)
No.NameCountTypeFull Name
1BMA6Ligand/IonBETA-D-MANNOSE
2HB22Ligand/Ion1-(4-AMINO-2-BUTYL-1H-IMIDAZO[4,5-C]QUINOLIN-1-YL)-2-METHYLPROPAN-2-OL
3MAN2Ligand/IonALPHA-D-MANNOSE
4NAG22Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:543 , GLY A:572 , VAL A:573 , THR A:574 , TYR B:348 , GLY B:351 , VAL B:378 , PHE B:405BINDING SITE FOR RESIDUE HB2 A 915
02AC2SOFTWARETYR A:348 , ILE A:349 , SER A:352 , VAL A:378 , PHE A:405 , ASP B:543 , ASP B:545 , GLY B:572 , THR B:574 , HOH B:1029BINDING SITE FOR RESIDUE HB2 B 901
03AC3SOFTWARELYS A:226 , PHE A:228 , 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 , TYR A:468 , HOH A:1088 , HOH A:1148 , HOH A:1190BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 293 RESIDUES 901 TO 904
04AC4SOFTWARESER A:368 , ARG A:370 , ASN A:395 , HOH A:1054 , TYR B:482 , GLY B:483 , ASP B:506 , ALA B:508 , LYS B:533 , HOH B:1086BINDING SITE FOR MONO-SACCHARIDE NAG A 905 BOUND TO ASN A 395
05AC5SOFTWARELYS A:476 , SER A:489 , LEU A:490 , ASN A:511 , ASP A:536 , HOH A:1085BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 511 RESIDUES 906 TO 908
06AC6SOFTWARESER A:522 , ASN A:546 , HOH A:1181BINDING SITE FOR MONO-SACCHARIDE NAG A 909 BOUND TO ASN A 546
07AC7SOFTWARELYS A:476 , GLN A:478 , TYR A:534 , ASP A:560 , VAL A:588 , ASN A:590 , GLU A:612 , VAL A:614 , HOH A:1081 , HOH A:1119 , HOH A:1161 , HOH A:1172 , HOH A:1180BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 590 RESIDUES 910 TO 912
08AC8SOFTWARELYS A:608 , SER A:609 , VAL A:611 , ASN A:640 , HOH A:1104 , GLN B:288 , ARG B:290BINDING SITE FOR MONO-SACCHARIDE NAG A 913 BOUND TO ASN A 640
09AC9SOFTWAREASN A:656 , ASN A:680 , THR A:682 , LEU A:683BINDING SITE FOR MONO-SACCHARIDE NAG A 914 BOUND TO ASN A 680
10BC1SOFTWARELYS B:243 , GLY B:244 , ASN B:285 , HOH B:1090 , HOH B:1101 , HOH B:1194BINDING SITE FOR MONO-SACCHARIDE NAG B 902 BOUND TO ASN B 285
11BC2SOFTWARELYS B:226 , SER B:230 , LEU B:250 , ASP B:252 , SER B:254 , TYR B:291 , ASN B:293 , ASP B:462 , HIS B:464 , SER B:465 , ASN B:466 , PHE B:467 , TYR B:468 , HOH B:1044 , HOH B:1102 , HOH B:1179BINDING SITE FOR CHAIN B OF SUGAR BOUND TO ASN B 293 RESIDUES 903 TO 906
12BC3SOFTWARETYR A:482 , ASP A:506 , ALA A:508 , LYS A:533 , HOH A:1195 , LEU B:367 , SER B:368 , ARG B:370 , ASN B:395BINDING SITE FOR MONO-SACCHARIDE NAG B 907 BOUND TO ASN B 395
13BC4SOFTWAREARG B:472 , LYS B:476 , SER B:489 , LEU B:490 , ASN B:511 , TYR B:534 , ASP B:536 , HOH B:1106 , HOH B:1119 , HOH B:1149BINDING SITE FOR CHAIN B OF SUGAR BOUND TO ASN B 511 RESIDUES 908 TO 910
14BC5SOFTWARESER B:522 , ASN B:546 , HOH B:1066 , HOH B:1163BINDING SITE FOR MONO-SACCHARIDE NAG B 911 BOUND TO ASN B 546
15BC6SOFTWAREGLN B:581 , ASN B:582BINDING SITE FOR MONO-SACCHARIDE NAG B 912 BOUND TO ASN B 582
16BC7SOFTWARELYS B:476 , GLN B:478 , TYR B:534 , ASP B:560 , ASN B:590 , GLU B:612 , HOH B:1050 , HOH B:1087 , HOH B:1137BINDING SITE FOR CHAIN B OF SUGAR BOUND TO ASN B 590 RESIDUES 913 TO 915
17BC8SOFTWAREGLN A:288 , ARG A:290 , HOH A:1099 , LYS B:608 , SER B:609 , ASN B:640 , HOH B:1082 , HOH B:1096 , HOH B:1143BINDING SITE FOR MONO-SACCHARIDE NAG B 916 BOUND TO ASN B 640
18BC9SOFTWAREASN B:656 , PHE B:678 , ASN B:680 , LEU B:683BINDING SITE FOR MONO-SACCHARIDE NAG B 917 BOUND TO ASN B 680

(-) SS Bonds  (12, 12)

Asymmetric/Biological 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
7B:36 -B:49
8B:181 -B:187
9B:257 -B:270
10B:260 -B:267
11B:479 -B:509
12B:776 -B:803

(-) Cis Peptide Bonds  (11, 11)

Asymmetric/Biological Unit
No.Residues
1Tyr A:34 -Pro A:35
2Asn A:42 -Asp A:43
3Asn A:97 -Pro A:98
4Pro A:432 -Leu A:433
5Ser A:805 -Pro A:806
6Tyr B:34 -Pro B:35
7Asn B:97 -Pro B:98
8Gly B:244 -Leu B:245
9Ser B:729 -Gly B:730
10Lys B:753 -Ser B:754
11Ser B:805 -Pro B:806

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4R6A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4R6A)

(-) Exons   (0, 0)

(no "Exon" information available for 4R6A)

(-) 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:746
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee....eeee...................ee.......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.....................eee....hhhhhh..................eee.........hhhhhhh......eee.........hhhhhhhh....eee...........hhhhh.....eee.....................eee.................eee.....ee.hhhhhhhhhhhhhh......hhhhh.eee............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4r6a A  31 SRSYPCDEKKQNDSVIAECSNRRLQEVPQTVGKYVTELDLSDNFITHITNESFQGLQNLTKINLNHNPNVNGLNITDGAFLNLKNLRELLLEDNQLPQIPSGLPESLTELSLIQNNIYNITKEGISRLINLKNLYLAWNCYFNKVCEKTNIEDGVFETLTNLELLSLSFNSLSHVPPKLPSSLRKLFLSNTQIKYISEEDFKGLINLTLLDLSGNCPRCFNAPFPCVPCDGGASINIDRFAFQNLTQLRYLNLSSTSLRKINAAWFKNMPHLKVLDLEFNYLVGEIASGAFLTMLPRLEILDLSFNYIKGSYPQHINISRNFSKLLSLRALHLRGYVFQELREDDFQPLMQLPNLSTINLGINFIKQIDFKLFQNFSNLEIIYLSENRISPLFEFDPHSNFYHFTRPLIKPQCAAYGKALDLSLNSIFFIGPNQFENLPDIACLNLSANSNAQVLSGTEFSAIPHVKYLDLTNNRLDFDNASALTELSDLEVLDLSYNSHYFRIAGVTHHLEFIQNFTNLKVLNLSHNNIYTLTDKYNLESKSLVELVFSGNRLDILWNDDDNRYISIFKGLKNLTRLDLSLNRLKHIPNEAFLNLPASLTELHINDNMLKFFNWTLLQQFPRLELLDLRGNKLLFLTDSLSDFTSSLRTLLLSHNRISHLPSGFLSEVSSLKHLDLSSNLLKTINKSATKLSMLELHGNPFECTCDIGDFRRWMDEHLNVKIPRLVDVICASPGDQRGKSIVSLE 818
                                    40        50        60        70        80        90       100|      121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431 ||    466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706       716       726       736       746       762       772       782       792       802       812      
                                                                                               100|                                                                                                                                                                                                                                                                                                                              433|                                                                                                                                                                                                                                                                                                     755|                                                        
                                                                                                112                                                                                                                                                                                                                                                                                                                               459                                                                                                                                                                                                                                                                                                      762                                                        


Chain B 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............eee.........ee............eee..................eee.......eehhhhhh......eee..............ee............eee..................eee.......eehhhhh.......eee.................hhhhh..ee............eee..........hhhhhh.....eee.....hhhhhhhhhhhhhh....eee................hhhhhhh....eee.......eehhhhhhhhh......eee.......ee.hhhhhhh....eee..........................hhhhhh..eeee...................eeeee......................eee.....................eee...hhhhhh.......hhhhhhh....eee.....................eee....hhhhhh..................eee.........hhhhhhh......eee.........hhhhhhhh....eee...........hhhhhh....eee.....................eee.................eee.....ee.hhhhhhhhhhhhhh......hhhhh.eee........... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4r6a B  31 SRSYPCDEKKQVIAECSNRRLQEVPQTVGKYVTELDLSDNFITHITNESFQGLQNLTKINLNHNPNVGLNITDGAFLNLKNLRELLLEDNQLPQIPSGLPESLTELSLIQNNIYNITKEGISRLINLKNLYLAWNCYFNKVCEKTNIEDGVFETLTNLELLSLSFNSLSHVPPKLPSSLRKLFLSNTQIKYISEEDFKGLINLTLLDLSGNCPRCFNAPFPCVPCDGGASINIDRFAFQNLTQLRYLNLSSTSLRKINAAWFKNMPHLKVLDLEFNYLVGEIASGAFLTMLPRLEILDLSFNYIKGSYPQHINISRNFSKLLSLRALHLRGYVFQELREDDFQPLMQLPNLSTINLGINFIKQIDFKLFQNFSNLEIIYLSENRISPLFEFDPHSNFYHFTRPLIKPQCAAYGKALDLSLNSIFFIGPNQFENLPDIACLNLSANSNAQVLSGTEFSAIPHVKYLDLTNNRLDFDNASALTELSDLEVLDLSYNSHYFRIAGVTHHLEFIQNFTNLKVLNLSHNNIYTLTDKYNLESKSLVELVFSGNRLDILWNDDDNRYISIFKGLKNLTRLDLSLNRLKHIPNEAFLNLPASLTELHINDNMLKFFNWTLLQQFPRLELLDLRGNKLLFLTDSLSDFTSSLRTLLLSHNRISHLPSGFLSEVSSLKHLDLSSNLLKTINKSTTKLSMLELHGNPFECTCDIGDFRRWMDEHLNVKIPRLVDVICASPGDQRGKSIVS 816
                                    40||      53        63        73        83        93      |115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750   ||  766       776       786       796       806       816
                                     41|                                                    100|                                                                                                                                                                                                                                                                                                                             433|                                                                                                                                                                                                                                                                                                    754|                                                       
                                      45                                                     113                                                                                                                                                                                                                                                                                                                              459                                                                                                                                                                                                                                                                                                     761
   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

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4R6A)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4R6A)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4R6A)

(-) Gene Ontology  (33, 33)

Asymmetric/Biological Unit(hide GO term definitions)

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  4r6a
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  TLR8_HUMAN | Q9NR97
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 Related Entries

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

UniProtKB/Swiss-Prot
        TLR8_HUMAN | Q9NR97: 3w3g 3w3j 3w3k 3w3l 3w3m 3w3n 3wn4 4qbz 4qc0 4r07 4r08 4r09 4r0a 5awa 5awb 5awc 5awd 5az5 5hdh

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4R6A)