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(-) Description

Title :  STRUCTURE REVEALS FUNCTION OF THE DUAL VARIABLE DOMAIN IMMUNOGLOBULIN (DVD-IG) MOLECULE
 
Authors :  C. G. Jakob, R. Edalji, R. A. Judge, E. Digiammarino, Y. Li, J. Gu, T. Ghay
Date :  12 Oct 12  (Deposition) - 08 May 13  (Release) - 08 May 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,H,L
Keywords :  Dfab Complex, Il-18, Dual Variable Domain Immunoglobulin, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. G. Jakob, R. Edalji, R. A. Judge, E. Digiammarino, Y. Li, J. Gu, T. Ghayur
Structure Reveals Function Of The Dual Variable Domain Immunoglobulin (Dvd-Ig[Tm]) Molecule
Mabs V. 5 358 2013
PubMed-ID: 23549062  |  Reference-DOI: 10.4161/MABS.23977

(-) Compounds

Molecule 1 - INTERLEUKIN-18
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIUDES 37-192
    Gene: IL18, IGIF, IL1F4
    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 - ANTI-IL12 ANTI-IL18 DFAB HEAVY CHAIN
    Chains: H
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Taxid: 9606
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - ANTI-IL12 ANTI-IL18 DFAB LIGHT CHAIN
    Chains: L
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Taxid: 9606
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : AHL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2GOL2Ligand/IonGLYCEROL
3SO41Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:143 , GLY A:144 , HOH A:345 , HOH A:357 , HOH A:369 , ARG H:100BINDING SITE FOR RESIDUE GOL A 201
2AC2SOFTWAREPHE H:24 , SER H:28 , LEU H:29 , SER H:30 , LYS H:73 , LYS H:77BINDING SITE FOR RESIDUE SO4 H 401
3AC3SOFTWAREPHE H:300 , PRO H:301 , SER H:311 , LEU H:312 , SER H:313 , GLN L:274 , SER L:276 , SER L:290 , SER L:291 , THR L:292 , HOH L:796BINDING SITE FOR RESIDUE GOL L 401
4AC4SOFTWARELYS L:45BINDING SITE FOR RESIDUE CL L 402

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1H:22 -H:97
2H:147 -H:221
3H:274 -H:330
4L:23 -L:88
5L:248 -L:308

(-) Cis Peptide Bonds  (11, 11)

Asymmetric/Biological Unit
No.Residues
1Ala A:78 -Pro A:79
2Arg A:94 -Gly A:95
3Trp H:55 -Asp H:56
4Gly H:124 -Pro H:125
5Phe H:280 -Pro H:281
6Glu H:282 -Pro H:283
7Ser L:7 -Pro L:8
8Ser L:94 -Pro L:95
9Ser L:120 -Pro L:121
10Trp L:207 -Pro L:208
11Tyr L:254 -Pro L:255

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4HJJ)

(-) 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 d4hjja_ A: automated matches                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..eeeee.....eeee.....eeee..hhhhhhhh.....eeeeeeee.....eeeeeeee...eeeeehhhhh.eeee.....ee........eeeee.......eeeee.....eeeeeeee..eeeeeeee.....hhhhh.eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hjj A  37 YFGKLESKLSVIRNLNDQVLFIDQGNRPLFEDMTDSDARDNAPRTIFIISMYKDSQPRGMAVTISVKAEKISTLSAENKIISFKEMNPPDNIKDTKSDIIFFQRSVPGHDNKMQFESSSYEGYFLAAEKERDLFKLILKKEDELGDRSIMFTVQNEA 193
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       


Chain H from PDB  Type:PROTEIN  Length:341
                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee.........eeeeeee......eeeeeee...eeee...hhh.eeeee.....eeeeee...hhhhheeeeeeee.....eeee...eeeee..........eeee...eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee........eeeee....eeeeee...hhhhheeeeeeee........eeee...eeeee........eeeee....eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.........eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hjj H   1 EVTLRESGPALVKPTQTLTLTCTFSGFSLSKSVMGVSWIRQPPGKALEWLAHIYWDDDKYYNPSLSARLTISKDTSKNQVVLTMTNMDPVDTATYYCARRGIRSAMDYWGQGTTVTVSSASTKGPEVQLVQSGTEVKKPGESLKISCKGSGYTVTSYWIGWVRQMPGKGLEWMGFIYPGDSETRYSPTFQGQVTISADKSFNTAFLQWSSLKASDTAMYYCARVGSGWYPYTFDIWGQGTMVTVSSASTKGPSVFPLAPSGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK 348
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260|      277       287       297       307       317       327       337       347 
                                                                                                                                                                                                                                                                                             260|                                                                                
                                                                                                                                                                                                                                                                                              268                                                                                


Chain L from PDB  Type:PROTEIN  Length:327
                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains d4hjjl1 L:1-113 automated matches                                                                                d4hjjl2 L:114-228 automated matches                                                                                d4hjjl3 L:229-327 automated matches                                                                 SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeee..........eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeeeeee..eeee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee....eeeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeeee......eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hjj L   1 DIVMTQSPDSLAVSLGERATINCKASQSVSNDVAWYQQKPGQPPKLLIYYASNRYTGVPDRFSGSGSGTDFTLTISSLEAEDVAVYYCQQDYNSPWTFGGGTKVEIKRTVAAPEIVMTQSPATLSVSPGERATLSCRASESISSNLAWYQQKPGQAPRLFIYTASTRATDIPARFSGSGSGTEFTLTISSLQSEDFAVYYCQQYNNWPSITFGQGTRLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE 327
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320
   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  (2, 4)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (34, 34)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ala A:78 - Pro A:79   [ RasMol ]  
    Arg A:94 - Gly A:95   [ RasMol ]  
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    Gly H:124 - Pro H:125   [ RasMol ]  
    Phe H:280 - Pro H:281   [ RasMol ]  
    Ser L:120 - Pro L:121   [ RasMol ]  
    Ser L:7 - Pro L:8   [ RasMol ]  
    Ser L:94 - Pro L:95   [ RasMol ]  
    Trp H:55 - Asp H:56   [ RasMol ]  
    Trp L:207 - Pro L:208   [ RasMol ]  
    Tyr L:254 - Pro L:255   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        IL18_HUMAN | Q14116: 1j0s 2vxt 3f62 3wo2 3wo3 3wo4 4eee 4ekx 4r6u 4xfs 4xft 4xfu

(-) Related Entries Specified in the PDB File

2vxv