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(-) Description

Title :  COMPLEX OF THE INTERLEUKIN-1 RECEPTOR WITH THE INTERLEUKIN-1 RECEPTOR ANTAGONIST (IL1RA)
 
Authors :  H. A. Schreuder, C. Tardif, S. Tramp-Kalmeyer, A. Soffientini, E. Saru A. Akeson, T. Bowlin, S. Yanofsky, R. W. Barrett
Date :  09 Apr 98  (Deposition) - 17 Jun 98  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  X,Y
Keywords :  Cytokine Receptor, Receptor Antagonist, Immunoglobulin Fold, Complex (Cytokine Receptor-Antagonist), Complex (Cytokine Receptor- Antagonist) Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Schreuder, C. Tardif, S. Trump-Kallmeyer, A. Soffientini, E. Sarubbi, A. Akeson, T. Bowlin, S. Yanofsky, R. W. Barrett
A New Cytokine-Receptor Binding Mode Revealed By The Crysta Structure Of The Il-1 Receptor With An Antagonist.
Nature V. 386 194 1997
PubMed-ID: 9062194  |  Reference-DOI: 10.1038/386194A0
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - INTERLEUKIN-1 RECEPTOR ANTAGONIST
    Cell Line: SF9
    Chains: X
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: TAC-BSP
    Expression System Taxid: 562
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: IL1RA
 
Molecule 2 - INTERLEUKIN-1 RECEPTOR
    Cell Line: SF9
    Chains: Y
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Cell Line: SF9
    Expression System Common: FALL ARMYWORM
    Expression System Plasmid: PVL1392
    Expression System Taxid: 7108
    Expression System Vector: BACULOVIRUS
    Fragment: TYPE I RECEPTOR, EXTRACELLULAR DOMAINS
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : XY

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR Y:102 , ALA Y:104 , GLY Y:172 , ASN Y:173 , GLU Y:194 , HOH Y:434BINDING SITE FOR RESIDUE NAG Y 401
2AC2SOFTWAREASN Y:213 , ALA Y:302 , TYR Y:304 , HOH Y:436BINDING SITE FOR RESIDUE NAG Y 402
3AC3SOFTWAREILE Y:227 , ASN Y:229 , HOH Y:455BINDING SITE FOR RESIDUE NAG Y 403
4AC4SOFTWAREASN Y:243 , HIS Y:288BINDING SITE FOR RESIDUE NAG Y 404

(-) SS Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1X:69 -X:116
2Y:3 -Y:84
3Y:24 -Y:76
4Y:101 -Y:144
5Y:122 -Y:176
6Y:228 -Y:292

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Val Y:64 -Pro Y:65
2Ser Y:210 -Pro Y:211

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Asymmetric/Biological Unit (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_049573A124TIL1RA_HUMANPolymorphism45507693XA99T
2UniProtVAR_019131A124GIL1R1_HUMANPolymorphism2228139YA104G
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1INTERLEUKIN_1PS00253 Interleukin-1 signature.IL1RA_HUMAN136-156  1X:111-131

(-) Exons   (0, 0)

(no "Exon" information available for 1IRA)

(-) 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 X from PDB  Type:PROTEIN  Length:145
 aligned with IL1RA_HUMAN | P18510 from UniProtKB/Swiss-Prot  Length:177

    Alignment length:145
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171     
          IL1RA_HUMAN    32 SSKMQAFRIWDVNQKTFYLRNNQLVAGYLQGPNVNLEEKIDVVPIEPHALFLGIHGGKMCLSCVKSGDETRLQLEAVNITDLSENRKQDKRFAFIRSDSGPTTSFESAACPGWFLCTAMEADQPVSLTNMPDEGVMVTKFYFQED 176
               SCOP domains d1irax_ X: Interleukin-1 receptor antagonist protein                                                                                              SCOP domains
               CATH domains 1iraX00 X:7-151  [code=2.80.10.50, no name defined]                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee....eeeee..eeeee...hhhhhh...eeeeeee..eeeee......eeeeeee..eeeeeee...hhh.....hhhhhheeeeeee..eeeeee......eee.........eee..hhh......eeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------T---------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------INTERLEUKIN_1        -------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ira X   7 SSKMQAFRIWDVNQKTFYLRNNQLVAGYLQGPNVNLEEKIDVVPIEPHALFLGIHGGKMCLSCVKSGDETRLQLEAVNITDLSENRKQDKRFAFIRSDSGPTTSFESAACPGWFLCTAMEADQPVSLTNMPDEGVMVTKFYFQED 151
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146     


Chain Y from PDB  Type:PROTEIN  Length:311
 aligned with IL1R1_HUMAN | P14778 from UniProtKB/Swiss-Prot  Length:569

    Alignment length:311
                                    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       330 
          IL1R1_HUMAN    21 DKCKEREEKIILVSSANEIDVRPCPLNPNEHKGTITWYKDDSKTPVSTEQASRIHQHKEKLWFVPAKVEDSGHYYCVVRNSSYCLRIKISAKFVENEPNLCYNAQAIFKQKLPVAGDGGLVCPYMEFFKNENNELPKLQWYKDCKPLLLDNIHFSGVKDRLIVMNVAEKHRGNYTCHASYTYLGKQYPITRVIEFITLEENKPTRPVIVSPANETMEVDLGSQIQLICNVTGQLSDIAYWKWNGSVIDEDDPVLGEDYYSVENPANKRRSTLITVLNISEIESRFYKHPFTCFAKNTHGIDAAYIQLIYPV 331
               SCOP domains d1iray1 Y:1-101 Type-1 interleukin-1 receptor                                                        d1iray2 Y:102-204 Type-1 interleukin-1 receptor                                                        d1iray3 Y:205-311 Type-1 interleukin-1 receptor                                                             SCOP domains
               CATH domains --1iraY01 Y:3-94 Immunoglobulins                                                              1iraY02 Y:95-200 Immunoglobulins                                                                          1iraY03 Y:201-311 Immunoglobulins                                                                               CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeee....eee.....hhh...eeeee...............eeee..eeee....hhh.eeeeeeeee..eeeeeeeeeeee.........hhh.eeeeee....eeee...hhhh..........eeee...........eeee..eeee....hhh.eeeeeeeeeee..eeeeeeeeeeeeee........eeee...eeee......eeeeeeeee....eeeeee...........eeeeeeee.....hhheeeeeeeee....hhhh...eeeeee....eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------G--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ira Y   1 DKCKEREEKIILVSSANEIDVRPCPLNPNEHKGTITWYKDDSKTPVSTEQASRIHQHKEKLWFVPAKVEDSGHYYCVVRNSSYCLRIKISAKFVENEPNLCYNAQAIFKQKLPVAGDGGLVCPYMEFFKNENNELPKLQWYKDCKPLLLDNIHFSGVKDRLIVMNVAEKHRGNYTCHASYTYLGKQYPITRVIEFITLEENKPTRPVIVSPANETMEVDLGSQIQLICNVTGQLSDIAYWKWNGSVIDEDDPVLGEDYYSVENPANKRRSTLITVLNISEIESRFYKHPFTCFAKNTHGIDAAYIQLIYPV 311
                                    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
   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  (2, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1IRA)

(-) Gene Ontology  (51, 56)

Asymmetric/Biological Unit(hide GO term definitions)
Chain X   (IL1RA_HUMAN | P18510)
molecular function
    GO:0005125    cytokine activity    Functions to control the survival, growth, differentiation and effector function of tissues and cells.
    GO:0045352    interleukin-1 Type I receptor antagonist activity    Blocks the binding of interleukin-1 to interleukin-1 Type I receptors.
    GO:0045353    interleukin-1 Type II receptor antagonist activity    Blocks the binding of interleukin-1 to interleukin-1 Type II receptors.
    GO:0005152    interleukin-1 receptor antagonist activity    Blocks the binding of interleukin-1 to the interleukin-1 receptor complex.
    GO:0005149    interleukin-1 receptor binding    Interacting selectively and non-covalently with the interleukin-1 receptor.
    GO:0005150    interleukin-1, Type I receptor binding    Interacting selectively and non-covalently with a Type I interleukin-1 receptor.
    GO:0005151    interleukin-1, Type II receptor binding    Interacting selectively and non-covalently with a Type II interleukin-1 receptor.
    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:0006953    acute-phase response    An acute inflammatory response that involves non-antibody proteins whose concentrations in the plasma increase in response to infection or injury of homeothermic animals.
    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:0030073    insulin secretion    The regulated release of proinsulin from secretory granules (B granules) in the B cells of the pancreas; accompanied by cleavage of proinsulin to form mature insulin.
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
    GO:0001960    negative regulation of cytokine-mediated signaling pathway    Any process that stops, prevents, or reduces the frequency, rate or extent of the cytokine mediated signaling pathway.
    GO:0034115    negative regulation of heterotypic cell-cell adhesion    Any process that stops, prevents, or reduces the frequency, rate, or extent of heterotypic cell-cell adhesion.
    GO:2000660    negative regulation of interleukin-1-mediated signaling pathway    Any process that stops, prevents or reduces the frequency, rate or extent of interleukin-1-mediated signaling pathway.
    GO:0051384    response to glucocorticoid    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a glucocorticoid stimulus. Glucocorticoids are hormonal C21 corticosteroids synthesized from cholesterol with the ability to bind with the cortisol receptor and trigger similar effects. Glucocorticoids act primarily on carbohydrate and protein metabolism, and have anti-inflammatory effects.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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.
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0031982    vesicle    Any small, fluid-filled, spherical organelle enclosed by membrane.

Chain Y   (IL1R1_HUMAN | P14778)
molecular function
    GO:0004908    interleukin-1 receptor activity    Combining with interleukin-1 to initiate a change in cell activity. Interleukin-1 is produced mainly by activated macrophages and is involved in the inflammatory response.
    GO:0004909    interleukin-1, Type I, activating receptor activity    Combining with interleukin-1 to initiate a change in cell activity via signaling pathways and mediated by adaptor proteins.
    GO:0035255    ionotropic glutamate receptor binding    Interacting selectively and non-covalently with an ionotropic glutamate receptor. Ionotropic glutamate receptors bind glutamate and exert an effect through the regulation of ion channels.
    GO:0005161    platelet-derived growth factor receptor binding    Interacting selectively and non-covalently with the platelet-derived growth factor receptor.
    GO:0002020    protease binding    Interacting selectively and non-covalently with any protease or peptidase.
    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).
    GO:0004871    signal transducer activity    Conveys a signal across a cell to trigger a change in cell function or state. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response.
    GO:0004888    transmembrane signaling receptor activity    Combining with an extracellular or intracellular signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity or state as part of signal transduction.
biological process
    GO:0007166    cell surface receptor signaling pathway    A series of molecular signals initiated by activation of a receptor on the surface of a cell. The pathway begins with binding of an extracellular ligand to a cell surface receptor, or for receptors that signal in the absence of a ligand, by ligand-withdrawal or the activity of a constitutively active receptor. The pathway ends with regulation of a downstream cellular process, e.g. transcription.
    GO:0071333    cellular response to glucose stimulus    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 a glucose stimulus.
    GO:0019221    cytokine-mediated signaling pathway    A series of molecular signals initiated by the binding of a cytokine to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0010286    heat acclimation    Any process that increases heat tolerance of an organism in response to high temperatures.
    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:0070498    interleukin-1-mediated signaling pathway    A series of molecular signals initiated by the binding of interleukin-1 to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0030728    ovulation    The release of a mature ovum/oocyte from an ovary.
    GO:0050727    regulation of inflammatory response    Any process that modulates the frequency, rate or extent of the inflammatory response, the immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents.
    GO:0070849    response to epidermal growth factor    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an epidermal growth factor stimulus.
    GO:0070555    response to interleukin-1    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an interleukin-1 stimulus.
    GO:0071731    response to nitric oxide    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nitric oxide stimulus.
    GO:0009314    response to radiation    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an electromagnetic radiation stimulus. Electromagnetic radiation is a propagating wave in space with electric and magnetic components. These components oscillate at right angles to each other and to the direction of propagation.
    GO:0071559    response to transforming growth factor beta    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a transforming growth factor beta stimulus.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
cellular component
    GO:0030424    axon    The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals and varicosities, which are sites of storage and release of neurotransmitter.
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    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.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0005887    integral component of plasma membrane    The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0014069    postsynaptic density of dendrite    An electron dense network of proteins within and adjacent to the postsynaptic membrane of the dendrite of asymetric synapses. Its major components include neurotransmitter receptors and the proteins that spatially and functionally organize them such as anchoring and scaffolding molecules, signaling enzymes and cytoskeletal components.
    GO:0043234    protein complex    A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.

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  1ira
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  IL1R1_HUMAN | P14778
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  IL1RA_HUMAN | P18510
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 Related Entries

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

UniProtKB/Swiss-Prot
        IL1R1_HUMAN | P14778: 1g0y 1itb 4dep 4gaf
        IL1RA_HUMAN | P18510: 1ilr 1ilt 1irp 1itn 2irt

(-) Related Entries Specified in the PDB File

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