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(-) Description

Title :  CRYSTAL STRUCTURE OF THE IL-18 SIGNALING TERNARY COMPLEX
 
Authors :  N. Tsutsumi, T. Kimura, K. Arita, M. Ariyoshi, H. Ohnishi, N. Kondo, M. S Z. Kato, H. Tochio
Date :  19 Dec 13  (Deposition) - 17 Dec 14  (Release) - 20 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Ternary Complex, Beta Trefoil Fold (Ligand), Three Immunoglobulin- Like Domains (Receptors), Immunity, Inflammation, Autoimmunity, Allergy, Glycosylation, Serum, Membrane, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Tsutsumi, T. Kimura, K. Arita, M. Ariyoshi, H. Ohnishi, T. Yamamoto X. Zuo, K. Maenaka, E. Y. Park, N. Kondo, M. Shirakawa, H. Tochio, Z. Kat
The Structural Basis For Receptor Recognition Of Human Interleukin-18
Nat Commun V. 5 5340 2014
PubMed-ID: 25500532  |  Reference-DOI: 10.1038/NCOMMS6340

(-) Compounds

Molecule 1 - INTERLEUKIN-18
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: IL18
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: IL-18, IBOCTADEKIN, INTERFERON GAMMA-INDUCING FACTOR, IFN- GAMMA-INDUCING FACTOR, INTERLEUKIN-1 GAMMA, IL-1 GAMMA
 
Molecule 2 - INTERLEUKIN-18 RECEPTOR 1
    Chains: B
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Common: FALL ARMYWORM
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Fragment: UNP RESIDUES 20-329
    Gene: IL18R1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: INTERLEUKIN-18 RECEPTOR ALPHA, IL-18R-1, IL-18R1, CD218 ANTIGEN-LIKE FAMILY MEMBER A, CDW218A, IL1 RECEPTOR-RELATED PROTEIN, IL-1RRP, IL1R-RP
 
Molecule 3 - INTERLEUKIN-18 RECEPTOR ACCESSORY PROTEIN
    Chains: C
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Common: FALL ARMYWORM
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Fragment: UNP RESIDUES 15-356
    Gene: IL18RAP
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: INTERLEUKIN-18 RECEPTOR BETA, IL-18 RECEPTOR ACCESSORY PROTEIN, IL-18RACP, ACCESSORY PROTEIN-LIKE, ACPL, CD218 ANTIGEN-LIKE FAMILY MEMBER B, CDW218B, IL-1R ACCESSORY PROTEIN-LIKE, IL-1RACPL, INTERLEUKIN-1 RECEPTOR 7, IL-1R-7, IL-1R7, INTERLEUKIN-18 RECEPTOR ACCESSORY PROTEIN-LIKE, IL-18R-BETA, IL-18RBETA

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 27)

Asymmetric/Biological Unit (5, 27)
No.NameCountTypeFull Name
1BMA4Ligand/IonBETA-D-MANNOSE
2CL1Ligand/IonCHLORIDE ION
3FUC2Ligand/IonALPHA-L-FUCOSE
4MAN3Ligand/IonALPHA-D-MANNOSE
5NAG17Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN B:91BINDING SITE FOR MONO-SACCHARIDE NAG B 901 BOUND TO ASN B 91
02AC2SOFTWAREASN B:102BINDING SITE FOR MONO-SACCHARIDE NAG B 902 BOUND TO ASN B 102
03AC3SOFTWAREGLY B:33 , ARG B:114 , LYS B:116 , HIS B:117 , SER B:118 , GLU B:122 , ASN B:150 , TYR B:182 , HIS B:190 , GLY B:193 , ASN B:197 , ASN B:203 , THR B:205 , ARG B:234 , ASN B:236 , SER B:238 , MET B:267 , LEU B:295 , ASN B:297 , FUC B:999 , MAN C:952BINDING SITE FOR CHAIN B OF SUGAR BOUND TO ASN B 150 RESIDUES 903 TO 998
04AC4SOFTWAREGLY B:33 , ARG B:114 , LYS B:116 , HIS B:117 , SER B:118 , GLU B:122 , TYR B:182 , ASN B:197 , ASN B:203 , THR B:205 , ARG B:234 , ASN B:236 , SER B:238 , MET B:267 , LEU B:295 , ASN B:297 , BMA B:955 , BMA B:958 , FUC B:999 , MAN C:952BINDING SITE FOR CHAIN B OF SUGAR BOUND TO ASN B 197 RESIDUES 905 TO 953
05AC5SOFTWARELYS B:116 , HIS B:117 , GLU B:122 , TYR B:182 , ASN B:203 , THR B:205 , ARG B:234 , ASN B:236 , SER B:238 , MET B:267 , LEU B:295 , ASN B:297 , NAG B:906 , BMA B:958 , FUC B:999 , MAN C:952BINDING SITE FOR CHAIN B OF SUGAR BOUND TO ASN B 203 RESIDUES 907 TO 955
06AC6SOFTWAREARG B:234 , ASN B:236 , SER B:238 , MET B:267BINDING SITE FOR CHAIN B OF SUGAR BOUND TO ASN B 236 RESIDUES 909 TO 910
07AC7SOFTWARELYS B:116 , HIS B:117 , HIS B:190 , GLY B:193 , LEU B:295 , ASN B:297 , NAG B:903 , NAG B:906 , NAG B:908BINDING SITE FOR CHAIN B OF SUGAR BOUND TO ASN B 297 RESIDUES 911 TO 999
08AC8SOFTWAREPRO C:116 , ASN C:119BINDING SITE FOR MONO-SACCHARIDE NAG C 901 BOUND TO ASN C 119
09AC9SOFTWAREGLU B:122 , ASN B:157 , GLN B:180 , TYR B:182 , ASN B:255 , GLY B:256 , NAG B:907 , NAG B:908 , ASN C:152 , ASP C:252 , ARG C:276 , ASP C:314 , PHE C:338 , GLN C:340 , ASN C:345 , HOH C:1009BINDING SITE FOR CHAIN C OF SUGAR BOUND TO ASN C 152 RESIDUES 902 TO 952
10BC1SOFTWAREASN B:255 , GLY B:256 , PHE C:338 , GLN C:340 , ASN C:345 , HOH C:1009BINDING SITE FOR CHAIN C OF SUGAR BOUND TO ASN C 345 RESIDUES 904 TO 905

(-) SS Bonds  (9, 9)

Asymmetric/Biological Unit
No.Residues
1B:22 -B:41
2B:43 -B:81
3B:119 -B:158
4B:140 -B:185
5B:237 -B:298
6C:46 -C:126
7C:155 -C:180
8C:175 -C:221
9C:273 -C:337

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Ala A:42 -Pro A:43
2Gly B:-2 -Pro B:-1
3Trp B:86 -Pro B:87
4Asp C:255 -Pro C:256
5Val C:302 -Pro C:303

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3WO4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3WO4)

(-) Exons   (0, 0)

(no "Exon" information available for 3WO4)

(-) 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:157
                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeee.....eeee.....eeee..hhhhhhhh.....eeeeeeee.....eeeeeeee...eeeeehhhhh.eee......ee........eeeeee..eeeeeeeee.....eeeeeeee..eeeeeeee.....hhhhh.eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wo4 A   1 YFGKLESKLSVIRNLNDQVLFIDQGNRPLFEDMTDSDCRDNAPRTIFIISMYKDSQPRGMAVTISVKCEKISTLSCENKIISFKEMNPPDNIKDTKSDIIFFQRSVPGHDNKMQFESSSYEGYFLACEKERDLFKLILKKEDELGDRSIMFTVQNED 157
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       


Chain B from PDB  Type:PROTEIN  Length:301
                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeee....eeee...............eeeee......ee........eeee..eeee...hhhhheeeeeee..eeeeeeeeee...............eeee...eeeee.........eeeeeeee..ee.........eeeee.hhhhheeeeeeeeeee..eeeeeeeeeeeeee........ee....eeeee......eeeeeeeee....eeeee..........eee...eeeee...eeeeeeeeee...hhhhh..eeeeeeee..eeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wo4 B  -2 GPESCTSRPHITVVEGEPFYLKHCSCSLAHEIETTTKSWYKSSGSQEHVELNPRSSSRIALHDCVLEFWPVELNDTGSYFFQMKNYTQKWKLNVIRRNKHSCFTERQVTSKIVEVKKFFQITCENSYYQTLVNSTSLYKNCKKLLLENNKNPTIKKNAEFEDQGYYSCVHFLHHNGKLFNITKTFNITIVEDRSNIVPVLLGPKLNHVAVELGKNVRLNCSALLNEEDVIYWMFGEENGSDPNIHEEKEMRIMTPEGKWHASKVLRIENIGESNLNVLYNCTVASTGGTDTKSFILVRKAD 318
                             ||     27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317 
                            -1|                                                                                                                                                                                                                                                                                                          
                             20                                                                                                                                                                                                                                                                                                          


Chain C from PDB  Type:PROTEIN  Length:270
                                                                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee....eeee..............ee..eeeee.......eeeee....eeeeeeeee............eeeee....eeee.hhhh.........eeeee..ee.......eeee...hhhhheeeeeeee........eeeeeeeeeee........eeee....eeee.....eeeeeeeeee.......eeeeeeee..eeee......eeeee...eeeeeeeeee...hhhhhh.eeeeeeee..eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3wo4 C  30 LLWTYSTRSEEEFVLFCDLPEPQKSPHIIQDKCTLHFLTPGVNNSGSYICRACCVKMILEVKPQTNASCEYSASHKQDLLLGSTGSISCPSLSCQSDAQSPAVTWYKNGKLLSVERSNRIVVDEVYDYHQGTYVCDYTQSDTVSSWTVRAVVQVRTIVGDTKLKPDILDPVEDTLEVELGKPLTISCKARFGFERVFNPVIKWYIKDSDLEWEVSVPEAKSIKSTLKDEIIERNIILEKVTQRDLRRKFVCFVQNSIGNTTQSVQLKEKR 356
                                    39        49    || 106       116       126||     146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356
                                                   54|                      127|                                                                                                                                                                                                                          
                                                   102                       138
   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 3WO4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3WO4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3WO4)

(-) Gene Ontology  (46, 58)

Asymmetric/Biological Unit(hide GO term definitions)

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  3wo4
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 Related Entries

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

UniProtKB/Swiss-Prot
        IL18R_HUMAN | Q13478: 3wo3 4r6u
        IL18_HUMAN | Q14116: 1j0s 2vxt 3f62 3wo2 3wo3 4eee 4ekx 4hjj 4r6u 4xfs 4xft 4xfu

(-) Related Entries Specified in the PDB File

3wo2 3wo3