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(-) Description

Title :  STRUCTURE OF A COMPLEX OF HUMAN IL-23 WITH 3 NANOBODIES (LLAMA VHHS)
 
Authors :  A. Desmyter, S. Spinelli, C. Button, M. Saunders, H. De Haard, H. Romme A. Union, C. Cambillau
Date :  27 Aug 12  (Deposition) - 19 Feb 14  (Release) - 16 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.55
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,I,J
Biol. Unit 1:  A,B,G,H,J  (1x)
Biol. Unit 2:  C,D,E,F,I  (1x)
Keywords :  Cytokine, Immunoglobulin Fold, Vhh Domain, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Desmyter, S. Spinelli, C. Button, M. Saunders, H. De Haard, H. Rommelaere, A. Union, C. Cambillau
Potent Multitopic Nanobody Inhibitors Of The Chronic Inflammation Promoting Cytokine Hil23.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - INTERLEUKIN-23 SUBUNIT ALPHA
    ChainsA, C
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System CommonFALL ARMYWORM
    Expression System Taxid7108
    Expression System Vector TypeBACULOVIRUS
    GeneIL23 P19, IL23A, SGRF, UNQ2498/PRO5798
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymIL-23 SUBUNIT ALPHA, IL-23-A, INTERLEUKIN-23 SUBUNIT P19, IL-23P19
 
Molecule 2 - INTERLEUKIN-12 SUBUNIT BETA
    ChainsB, D
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System CommonFALL ARMYWORM
    Expression System Taxid7108
    Expression System Vector TypeBACULOVIRUS
    GeneIL12 P40, IL12B, NKSF2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymIL-12B, CYTOTOXIC LYMPHOCYTE MATURATION FACTOR 40 KDA SUBUNIT, CLMF P40, IL-12 SUBUNIT P40, NK CELL STIMULATORY FACTOR CHAIN 2, NKSF2
 
Molecule 3 - NANOBODY 124C4
    ChainsE, G
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21
    Expression System Taxid511693
    Organism ScientificLAMA GLAMA
    Organism Taxid9844
 
Molecule 4 - NANOBODY 37D5
    ChainsF, J
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21
    Expression System Taxid511693
    Organism ScientificLAMA GLAMA
    Organism Taxid9844
 
Molecule 5 - NANOBODY 22E11
    ChainsH, I
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21
    Expression System Taxid511693
    Organism ScientificLAMA GLAMA
    Organism Taxid9844

 Structural Features

(-) Chains, Units

  12345678910
Asymmetric Unit ABCDEFGHIJ
Biological Unit 1 (1x)AB    GH J
Biological Unit 2 (1x)  CDEF  I 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 10)

Asymmetric Unit (3, 10)
No.NameCountTypeFull Name
1BMA2Ligand/IonBETA-D-MANNOSE
2MAN4Ligand/IonALPHA-D-MANNOSE
3NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (3, 5)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2MAN2Ligand/IonALPHA-D-MANNOSE
3NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (3, 5)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2MAN2Ligand/IonALPHA-D-MANNOSE
3NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETRP B:2 , GLU B:12 , NAG B:402 , BMA B:403BINDING SITE FOR RESIDUE NAG B 401
02AC2SOFTWARETRP B:2 , GLU B:12 , HIS B:83 , TYR B:198 , ASN B:200 , NAG B:401 , HOH B:584BINDING SITE FOR RESIDUE NAG B 402
03AC3SOFTWARENAG B:401 , MAN B:404 , MAN B:405BINDING SITE FOR RESIDUE BMA B 403
04AC4SOFTWAREGLU B:3 , BMA B:403BINDING SITE FOR RESIDUE MAN B 404
05AC5SOFTWAREBMA B:403 , GLU D:100BINDING SITE FOR RESIDUE MAN B 405
06AC6SOFTWARETRP D:2 , GLU D:12 , NAG D:402 , BMA D:403 , HOH D:675BINDING SITE FOR RESIDUE NAG D 401
07AC7SOFTWARETRP D:2 , GLU D:12 , HIS D:83 , TYR D:198 , ASN D:200 , NAG D:401 , HOH D:646BINDING SITE FOR RESIDUE NAG D 402
08AC8SOFTWARENAG D:401 , MAN D:404 , MAN D:405BINDING SITE FOR RESIDUE BMA D 403
09AC9SOFTWAREGLU D:3 , BMA D:403 , HOH D:554BINDING SITE FOR RESIDUE MAN D 404
10BC1SOFTWAREBMA D:403 , HOH D:629BINDING SITE FOR RESIDUE MAN D 405

(-) SS Bonds  (17, 17)

Asymmetric Unit
No.Residues
1A:58 -A:70
2B:28 -B:68
3B:109 -B:120
4B:148 -B:171
5B:278 -B:305
6C:58 -C:70
7D:28 -D:68
8D:109 -D:120
9D:148 -D:171
10D:278 -D:305
11E:22 -E:96
12F:22 -F:96
13F:50 -F:102
14G:22 -G:92
15H:22 -H:96
16I:22 -I:96
17J:50 -J:102

(-) Cis Peptide Bonds  (13, 13)

Asymmetric Unit
No.Residues
1Glu A:93 -Pro A:94
2Trp A:137 -Gln A:138
3Ala B:19 -Pro B:20
4Glu B:100 -Pro B:101
5Thr B:242 -Pro B:243
6Glu C:93 -Pro C:94
7Ser C:169 -Pro C:170
8Ala D:19 -Pro D:20
9Thr D:242 -Pro D:243
10Ser G:25 -Gly G:26
11Phe H:102 -Pro H:103
12Phe I:102 -Pro I:103
13Asn J:110 -Gly J:111

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4GRW)

(-) 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:130
                                                                                                                                                                   
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhh........hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------- Transcript
                4grw A    8 SPAWTQCQQLSQKLCTLAWSAHPLNDVPHIQCGDGCDPQGLRDNSQFCLQRIHQGLIFYEKLLGSDIFTGEPSLLPDSPVGQLHASLLGLSQLLQPQPWQRLLLRFKILRSLQAFVAVAARVFAHGAATL  168
                                    17        27   ||   52        62        72        82        92       102       112     ||138       148       158       168
                                                  31|                                                                    118|                                 
                                                   47                                                                     135                                 

Chain B from PDB  Type:PROTEIN  Length:293
                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..eeeeeee.......eeeeee.........eeee.......ee..eeeeee.hhhhheeeeeee..eeeeeeeeeeeeee..ee.................eee......eeeeeeee.....eeeeeeeee....eee...eeeeee....eeeeeeeeee............eeeeeeeee..eeeeeeeeehhhhh......eeeeeee.....eeeeeee.............eeeeeeee..eeee...eeeee.....eeeeeeee..........eeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4grw B    1 IWELKKDVYVVELDWYPDAPGEMVVLTCDTPEEDGITWTLDQSSEVLGSGKTLTIQVKEFGDAGQYTCHKGGEVLSHSLLLLHKKEDGIWSTDILKDQKEPKNKTFLRCEAKNYSGRFTCWWLTTISTDLTFSVKSSRGPQGVTCGAATLSAERVRNKEYEYSVECQEDSACPAAEESLPIEVMVDAVHKLKYENYTSSFFIRDIIKPDPPKNLQLKPLKNSRQVEVSWEYPDTWSTPHSYFSLTFCVQVQGDRVFTDKTSATVICRKNASISVRAQDRYYSSSWSEWASVPC  305
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       143       153     ||165       175       185       195       205       215       225       235       245       255 ||    272       282       292       302   
                                                                                                                                                                    139|             159|                                                                                            257|                                        
                                                                                                                                                                     143              162                                                                                             265                                        

Chain C from PDB  Type:PROTEIN  Length:129
                                                                                                                                                                  
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhh.......hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                4grw C    9 PAWTQCQQLSQKLCTLAWSAHPLDVPHIQCGDGCDPQGLRDNSQFCLQRIHQGLIFYEKLLGSDIFTGEPSLLPDSPVGQLHASLLGLSQLLQQPWQRLLLRFKILRSLQAFVAVAARVFAHGAATLSP  170
                                    18        28  ||    54        64        74        84        94       104       114  ||   141       151       161         
                                                 31|                                                                  117|                                   
                                                  48                                                                   135                                   

Chain D from PDB  Type:PROTEIN  Length:292
                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..eeeeeee.......eeeeee.........eeee.......ee..eeeeee.hhhhheeeeeee..eeeeeeeeeeeeee..ee.................eee......eeeeeeee.....eeeeeeeee.....eeeee...eeeeee....eeeeeeeeee............eeeeeeeee..eeeeeeeeehhhhh......eeeeee...eeeeee.............eeeeeeee..eeee...eeee......eeeeeeee..........eeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4grw D    1 IWELKKDVYVVELDWYPDAPGEMVVLTCDTPEEDGITWTLDQSSEVLGSGKTLTIQVKEFGDAGQYTCHKGGEVLSHSLLLLHKKEDGIWSTDILKDQKEPKNKTFLRCEAKNYSGRFTCWWLTTISTDLTFSVKSSRGSSDPQGVTCGAATLSAERVRNKEYEYSVECQEDSACPAAEESLPIEVMVDAVHKLKYENYTSSFFIRDIIKPDPPKNLQLKPLQVEVSWEYPDTWSTPHSYFSLTFCVQVQGDRVFTDKTSATVICRKNASISVRAQDRYYSSSWSEWASVPC  305
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       162       172       182       192       202       212       222 ||    236       246       256||     273       283       293       303  
                                                                                                                                                                                        159|                                                           224|                         257|                                        
                                                                                                                                                                                         162                                                            229                          265                                        

Chain E from PDB  Type:PROTEIN  Length:125
                                                                                                                                                              
               SCOP domains d4grwe_ E: automated matches                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhhhh.eeeeee.....eeeeeeee....eeee.......eeeeee....eeeeee...hhhhheeeeeeee........hhh.eeee...eeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                4grw E    1 EVQLVESGGGLVQPGGSLRLSCAASGFTLDDYAIAWFRQAPGKEREGVSGIDSGDGSAYYADSVKGRFTISSDNAKNTVYLQMNSLRPEDTAVYYCARVRTGWGLNAPDYAMDYWGKGTLVTVSS  125
                                    10        20        30        40        50        60        70        80        90       100       110       120     

Chain F from PDB  Type:PROTEIN  Length:125
                                                                                                                                                              
               SCOP domains d4grwf_ F: automated matches                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee..eee.....eeeeee..........eeeeee......eeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeee...hhhhhh............eeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                4grw F    2 VQLVESGGGLVQPGGSLRLSCAASGFTLDYLAIGWFRQAPGKEREGVSCVSSSGQYTYYADSVKGRFTISRDNAESTVYLQMNSLKPEDTAVYYCATDPECYRVRGYYNGEYDYWGQGTQVTVSS  126
                                    11        21        31        41        51        61        71        81        91       101       111       121     

Chain G from PDB  Type:PROTEIN  Length:125
                                                                                                                                                              
               SCOP domains d4grwg_ G: automated matches                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhh.eeeeeee......eeeeeee.....eee.......eeeeee....eeeeee...hhhhheeeeeeee........hhh.eeee...eeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                4grw G    1 EVQLVESGGGLVQPGGSLRLSCAASGFTLDDYAIAWFRQAPGKEREGVSGIDSGDGSAYYADSVKGRFTISSDNAKNTVYLQMNSLRPEDTAVYYCARVRTGWGLNAPDYAMDYWGKGTLVTVSS  121
                                    10        20       28B|       36        46        56        66        76        86        96       106       116     
                                                     27B|||                                                                                              
                                                      28C||                                                                                              
                                                       28B|                                                                                              
                                                        28A                                                                                              

Chain H from PDB  Type:PROTEIN  Length:123
                                                                                                                                                            
               SCOP domains d4grwh_ H: automated matches                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee....eeeeeee........eeeeeee......eeeeeee..eeeeee.hhhh..eeeeee....eeeeee...hhhhheeeeeeee......hhh.eeee...eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                4grw H    1 EVQLVESGGGLVQAGGSLRLSCAASGRTFSWSAVGWFRQAPGKEREFVAAIRWSGGSPYYADSVKDRFTISRDNAKNTVYLQMNSLRPEDTAVYLCGETSLFPTSRGSHYDTWGQGTQVTVSS  123
                                    10        20        30        40        50        60        70        80        90       100       110       120   

Chain I from PDB  Type:PROTEIN  Length:123
                                                                                                                                                            
               SCOP domains --------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee....eeeeeee........eeeeeee......eeeeeee......ee.......eeeeee....eeeeee...hhhhheeeeeeee......hhh.eeee...eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                4grw I    1 EVQLVESGGGLVQAGGSLRLSCAASGRTFSWSAVGWFRQAPGKEREFVAAIRWSGGSPYYADSVKDRFTISRDNAKNTVYLQMNSLRPEDTAVYLCGETSLFPTSRGSHYDTWGQGTQVTVSS  123
                                    10        20        30        40        50        60        70        80        90       100       110       120   

Chain J from PDB  Type:PROTEIN  Length:122
                                                                                                                                                           
               SCOP domains d4grwj_ J: automated matches                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..eee.....eeeeeee.........eeeeee......eeeeee......eee.......eeeee.....eeeeee...hhhhheeeeeee...hhhhhh..........eeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                4grw J    3 QLVESGGGLVQPGGSLRLSCAASGFTLDYLAIGWFRQAPGKEREGVSCVSSSGQYTYYADSVKGRFTISRDNAESTVYLQMNSLKPEDTAVYYCATDPECYRVRGYYNGDYWGQGTQVTVSS  126
                                    12        22        32        42        52        62        72        82        92       102      |114       124  
                                                                                                                                   109A ||            
                                                                                                                                      111|            
                                                                                                                                       114            

   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  (1, 5)

Asymmetric Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (77, 108)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        IL12B_HUMAN | P294601f42 1f45 3d85 3d87 3duh 3hmx 3qwr 5mj3 5mj4
        IL23A_HUMAN | Q9NPF73d85 3d87 3duh 3qwr 5mj3 5mj4

(-) Related Entries Specified in the PDB File

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