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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN IL-18 COMPLEXED TO MURINE REFERENCE ANTIBODY 125-2H FAB
 
Authors :  M. A. Argiriadi, T. Xiang, C. Wu, T. Ghayur, D. W. Borhani
Date :  10 Jul 08  (Deposition) - 23 Jun 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.49
Chains :  Asym./Biol. Unit :  H,I,L
Keywords :  Fab, Il-18, Secreted, Cytokine, Autoimmunity, Glycoprotein, Th1/Th2 Cells, Immunoglobulin Domain, Immunoglobulin V Region (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. A. Argiriadi, T. Xiang, C. Wu, T. Ghayur, D. W. Borhani
Unusual Water-Mediated Antigenic Recognition Of The Proinflammatory Cytokine Interleukin-18.
J. Biol. Chem. V. 284 24478 2009
PubMed-ID: 19553661  |  Reference-DOI: 10.1074/JBC.M109.023887

(-) Compounds

Molecule 1 - MURINE IGG 125-2H
    Cell LineHYBRIDOMA
    ChainsH
    EngineeredYES
    Expression SystemMUS MUSCULUS
    Expression System Taxid10090
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
 
Molecule 2 - INTERLEUKIN-18
    ChainsI
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21
    Expression System Taxid511693
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymIL-18, INTERFERON-GAMMA-INDUCING FACTOR, IFN-GAMMA-INDUCING FACTOR, INTERLEUKIN-1 GAMMA, IL-1 GAMMA, IBOCTADEKIN
 
Molecule 3 - MURINE IGG 125-2H
    Cell LineHYBRIDOMA
    ChainsL
    EngineeredYES
    Expression SystemMUS MUSCULUS
    Expression System Taxid10090
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit HIL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2MG1Ligand/IonMAGNESIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR H:59 , ARG H:64BINDING SITE FOR RESIDUE CL H1214
2AC2SOFTWAREHIS I:145 , ASP I:146 , ASN I:147 , LYS I:148 , HOH I:2081BINDING SITE FOR RESIDUE CL I1193
3AC3SOFTWAREHOH I:2042 , HOH I:2069 , HOH I:2070BINDING SITE FOR RESIDUE MG I1194

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1H:22 -H:92
2H:140 -H:195
3L:23 -L:88
4L:134 -L:194

(-) Cis Peptide Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1Phe H:146 -Pro H:147
2Glu H:148 -Pro H:149
3Trp H:188 -Pro H:189
4Ala I:78 -Pro I:79
5Ser L:7 -Pro L:8
6Ser L:94 -Pro L:95
7Tyr L:140 -Pro L:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2VXT)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2VXT)

(-) Exons   (3, 3)

Asymmetric/Biological Unit (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002803571aENSE00001370484chr11:112034840-112034629212IL18_HUMAN-00--
1.2bENST000002803572bENSE00002187737chr11:112025784-11202569887IL18_HUMAN1-27270--
1.3aENST000002803573aENSE00001682610chr11:112024326-11202431512IL18_HUMAN27-3150--
1.4cENST000002803574cENSE00000996283chr11:112020929-112020795135IL18_HUMAN31-76461I:37-7640
1.5ENST000002803575ENSE00000996284chr11:112019459-112019326134IL18_HUMAN76-120451I:76-12045
1.6eENST000002803576eENSE00002192330chr11:112014540-112013974567IL18_HUMAN121-193731I:121-19272

(-) 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 H from PDB  Type:PROTEIN  Length:207
                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2vxtH01 H:1-113 Immunoglobulins                                                                                  2vxtH02 H:114-212 Immunoglobulins                                                            - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhh..eeeeeee...eeeeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeee...ee...eeeee........eeeee....eeeeeeeeeee.....eeee.hhh....eee...ee....eeeeeeeeee.........eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vxt H   1 EIQLQQSGPELVKPGASVKVSCKASGYSFTDYFIYWVKQSHGKSLEWIGDIDPYNGDTSYNQKFRDKATLTVDQSSTTAFMHLNSLTSEDSAVYFCARGLRFWGQGTLVTVSAAKTTPPSVYPLAPGSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPR 213
                                    10        20        30        40        50  |     59        69        79   |||  86        96|      110       120      |136       146       156       166       176       186       196       206       
                                                                              52A                            82A||            96|                       127|                                                                               
                                                                                                              82B|            101                        134                                                                               
                                                                                                               82C                                                                                                                         

Chain I from PDB  Type:PROTEIN  Length:156
 aligned with IL18_HUMAN | Q14116 from UniProtKB/Swiss-Prot  Length:193

    Alignment length:156
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186      
           IL18_HUMAN    37 YFGKLESKLSVIRNLNDQVLFIDQGNRPLFEDMTDSDCRDNAPRTIFIISMYKDSQPRGMAVTISVKCEKISTLSCENKIISFKEMNPPDNIKDTKSDIIFFQRSVPGHDNKMQFESSSYEGYFLACEKERDLFKLILKKEDELGDRSIMFTVQNE 192
               SCOP domains d2vxti_ I: automated matches                                                                                                                                 SCOP domains
               CATH domains 2vxtI00 I:37-192  [code=2.80.10.50, no name defined]                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .ee..eeeeeeee.....eeee.....eeee..hhhhhhhh.....eeeeeeeee...eeeeeeeee...eeeeehhhhh.eeee.....ee........eeeeee..eeeeeeeee.....eeeeeeee..eeeeeeee......hhhh.eeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.4c  PDB: I:37-76 UniProt: 31-76  --------------------------------------------Exon 1.6e  PDB: I:121-192 UniProt: 121-193 [INCOMPLETE]                  Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------Exon 1.5  PDB: I:76-120 UniProt: 76-120      ------------------------------------------------------------------------ Transcript 1 (2)
                 2vxt I  37 YFGKLESKLSVIRNLNDQVLFIDQGNRPLFEDMTDSDARDNAPRTIFIISMYKDSQPRGMAVTISVKAEKISTLSAENKIISFKEMNPPDNIKDTKSDIIFFQRSVPGHDNKMQFESSSYEGYFLAAEKERDLFKLILKKEDELGDRSIMFTVQNE 192
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186      

Chain L from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains d2vxtl1 L:1-107 automated matches                                                                          d2vxtl2 L:108-213 automated matches                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------2vxtL02 L:109-211 Immunoglobulins                                                                      -- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee.....eeeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vxt L   1 DIQMTQSPSSLSASLGERVSLTCRASQDIGSKLYWLQQEPDGTFKRLIYATSSLDSGVPKRFSGSRSGSDYSLTISSLESEDFVDYYCLQYASSPYTFGGGTKLAIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE 213
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210   

   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  (3, 3)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2VXT)

(-) Gene Ontology  (34, 34)

Asymmetric/Biological Unit(hide GO term definitions)
Chain I   (IL18_HUMAN | Q14116)
molecular function
    GO:0005125    cytokine activity    Functions to control the survival, growth, differentiation and effector function of tissues and cells.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0000165    MAPK cascade    An intracellular protein kinase cascade containing at least a MAPK, a MAPKK and a MAP3K. The cascade can also contain two additional tiers: the upstream MAP4K and the downstream MAP Kinase-activated kinase (MAPKAPK). The kinases in each tier phosphorylate and activate the kinases in the downstream tier to transmit a signal within a cell.
    GO:0042088    T-helper 1 type immune response    An immune response which is associated with resistance to intracellular bacteria, fungi, and protozoa, and pathological conditions such as arthritis, and which is typically orchestrated by the production of particular cytokines by T-helper 1 cells, most notably interferon-gamma, IL-2, and lymphotoxin.
    GO:0001525    angiogenesis    Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels.
    GO:0007267    cell-cell signaling    Any process that mediates the transfer of information from one cell to another. This process includes signal transduction in the receiving cell and, where applicable, release of a ligand and any processes that actively facilitate its transport and presentation to the receiving cell. Examples include signaling via soluble ligands, via cell adhesion molecules and via gap junctions.
    GO:0071407    cellular response to organic cyclic compound    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic cyclic compound stimulus.
    GO:0042033    chemokine biosynthetic process    The chemical reactions and pathways resulting in the formation of chemokines, any member of a family of small chemotactic cytokines; their name is derived from their ability to induce directed chemotaxis in nearby responsive cells. All chemokines possess a number of conserved cysteine residues involved in intramolecular disulfide bond formation. Some chemokines are considered pro-inflammatory and can be induced during an immune response to recruit cells of the immune system to a site of infection, while others are considered homeostatic and are involved in controlling the migration of cells during normal processes of tissue maintenance or development. Chemokines are found in all vertebrates, some viruses and some bacteria.
    GO:0042253    granulocyte macrophage colony-stimulating factor biosynthetic process    The chemical reactions and pathways resulting in the formation of granulocyte macrophage colony-stimulating factor, cytokines that act in hemopoiesis by controlling the production, differentiation, and function of two related white cell populations, granulocytes and monocytes-macrophages.
    GO:0006955    immune response    Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
    GO:0006954    inflammatory response    The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
    GO:0042095    interferon-gamma biosynthetic process    The chemical reactions and pathways resulting in the formation of interferon-gamma. Interferon gamma is the only member of the type II interferon found so far.
    GO:0042231    interleukin-13 biosynthetic process    The chemical reactions and pathways resulting in the formation of interleukin-13.
    GO:0042094    interleukin-2 biosynthetic process    The chemical reactions and pathways resulting in the formation of interleukin-2.
    GO:0031663    lipopolysaccharide-mediated signaling pathway    A series of molecular signals initiated by the binding of a lipopolysaccharide (LPS) to a receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription. Lipopolysaccharides are major components of the outer membrane of Gram-negative bacteria, making them prime targets for recognition by the immune system.
    GO:0030101    natural killer cell activation    The change in morphology and behavior of a natural killer cell in response to a cytokine, chemokine, cellular ligand, or soluble factor.
    GO:0045662    negative regulation of myoblast differentiation    Any process that stops, prevents, or reduces the frequency, rate or extent of myoblast differentiation. A myoblast is a mononucleate cell type that, by fusion with other myoblasts, gives rise to the myotubes that eventually develop into skeletal muscle fibers.
    GO:0042346    positive regulation of NF-kappaB import into nucleus    Any process that activates or increases the frequency, rate or extent of transfer of NF-kappaB, a transcription factor for eukaryotic RNA polymerase II promoters, from the cytoplasm into the nucleus, across the nuclear membrane.
    GO:0051142    positive regulation of NK T cell proliferation    Any process that activates or increases the frequency, rate or extent of natural killer T cell proliferation.
    GO:0042104    positive regulation of activated T cell proliferation    Any process that activates or increases the rate or extent of activated T cell proliferation.
    GO:0010628    positive regulation of gene expression    Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:0032725    positive regulation of granulocyte macrophage colony-stimulating factor production    Any process that activates or increases the frequency, rate, or extent of granulocyte macrophage colony-stimulating factor production.
    GO:0050729    positive regulation of inflammatory response    Any process that activates or increases the frequency, rate or extent of the inflammatory response.
    GO:0032729    positive regulation of interferon-gamma production    Any process that activates or increases the frequency, rate, or extent of interferon-gamma production. Interferon-gamma is also known as type II interferon.
    GO:0032740    positive regulation of interleukin-17 production    Any process that activates or increases the frequency, rate, or extent of production of any member of the interleukin-17 family of cytokines.
    GO:0032819    positive regulation of natural killer cell proliferation    Any process that activates or increases the frequency, rate or extent of natural killer cell proliferation.
    GO:0034105    positive regulation of tissue remodeling    Any process that activates or increases the frequency, rate, or extent of tissue remodeling.
    GO:0030155    regulation of cell adhesion    Any process that modulates the frequency, rate or extent of attachment of a cell to another cell or to the extracellular matrix.
    GO:0030431    sleep    Any process in which an organism enters and maintains a periodic, readily reversible state of reduced awareness and metabolic activity. Usually accompanied by physical relaxation, the onset of sleep in humans and other mammals is marked by a change in the electrical activity of the brain.
    GO:0042092    type 2 immune response    An immune response which is associated with resistance to extracellular organisms such as helminths and pathological conditions such as allergy, which is orchestrated by the production of particular cytokines, most notably IL-4, IL-5, IL-10, and IL-13, by any of a variety of cell types including T-helper 2 cells, eosinophils, basophils, mast cells, and nuocytes, resulting in enhanced production of certain antibody isotypes and other effects.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.

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 Related Entries

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

UniProtKB/Swiss-Prot
        IL18_HUMAN | Q141161j0s 3f62 3wo2 3wo3 3wo4 4eee 4ekx 4hjj 4r6u 4xfs 4xft 4xfu

(-) Related Entries Specified in the PDB File

1j0s SOLUTION STRUCTURE OF THE HUMAN INTERLEUKIN- 18
2vxu CRYSTAL STRUCTURE OF MURINE REFERENCE ANTIBODY 125-2H FAB FRAGMENT
2vxv CRYSTAL STRUCTURE OF HUMAN IGG ABT-325 FAB FRAGMENT