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(-) Description

Title :  CRYSTAL STRUCTURE OF THE IL-22/IL-22R1 COMPLEX
 
Authors :  L. Bleicher, P. R. De Moura, L. Watanabe, D. Colau, L. Dumoutier, J. - C. Renauld, I. Polikarpov
Date :  28 Jun 08  (Deposition) - 19 Aug 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  I,R
Keywords :  Cytokine-Receptor Complex, Fibronectin-Iii, Cytokine, Glycoprotein, Polymorphism, Secreted, Membrane, Receptor, Transmembrane, Cytokine/Cytokine Receptor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. Bleicher, P. R. De Moura, L. Watanabe, D. Colau, L. Dumoutier, J. -C. Renauld, I. Polikarpov
Crystal Structure Of The Il-22/Il-22R1 Complex And Its Implications For The Il-22 Signaling Mechanism
Febs Lett. V. 582 2985 2008
PubMed-ID: 18675809  |  Reference-DOI: 10.1016/J.FEBSLET.2008.07.046
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - INTERLEUKIN-22
    ChainsI
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET3A
    Expression System StrainBL21-AI
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentCYTOKINE, UNP RESIDUES 29-179
    GeneIL22
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymIL-22, IL-10-RELATED T-CELL-DERIVED-INDUCIBLE FACTOR, IL-TIF
 
Molecule 2 - INTERLEUKIN-22 RECEPTOR SUBUNIT ALPHA-1
    ChainsR
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET3A
    Expression System StrainBL21-AI
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentSOLUBLE PORTION, UNP RESIDUES 18-228
    GeneIL22RA1
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymIL-22R-ALPHA-1, CYTOKINE RECEPTOR FAMILY 2 MEMBER 9, CRF2-9

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit IR

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3DLQ)

(-) Sites  (0, 0)

(no "Site" information available for 3DLQ)

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1I:89 -I:178
2R:71 -R:79
3R:128 -R:217

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gln I:112 -Pro I:113
2Gly R:47 -Thr R:48

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (5, 5)

Asymmetric/Biological Unit (5, 5)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_039699S130PI22R1_HUMANPolymorphism34900099RS130P
2UniProtVAR_013078S158GIL22_HUMANPolymorphism2227507IS158G
3UniProtVAR_039700V205II22R1_HUMANPolymorphism16829204RV205I
4UniProtVAR_039701A209SI22R1_HUMANPolymorphism34379702RA209S
5UniProtVAR_039702L222PI22R1_HUMANPolymorphism34782294RL222P

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1INTERLEUKIN_10PS00520 Interleukin-10 family signature.IL22_HUMAN84-104  1I:84-104

(-) Exons   (5, 5)

Asymmetric/Biological Unit (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003280871ENSE00001303127chr12:68647284-68647043242IL22_HUMAN1-62621I:40-6223
1.2ENST000003280872ENSE00000920698chr12:68646609-6864654466IL22_HUMAN63-84221I:63-8422
1.3ENST000003280873ENSE00000920697chr12:68646427-68646284144IL22_HUMAN85-132481I:85-13046
1.4ENST000003280874ENSE00001100627chr12:68645358-6864529366IL22_HUMAN133-154221I:140-15415
1.5ENST000003280875ENSE00001311233chr12:68642656-68642025632IL22_HUMAN155-179251I:155-17925

(-) 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 I from PDB  Type:PROTEIN  Length:131
 aligned with IL22_HUMAN | Q9GZX6 from UniProtKB/Swiss-Prot  Length:179

    Alignment length:140
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179
           IL22_HUMAN    40 CRLDKSNFQQPYITNRTFMLAKEASLADNNTDVRLIGEKLFHGVSMSERCYLMKQVLNFTLEEVLFPQSDRFQPYMQEVVPFLARLSNRLSTCHIEGDDLHIQRNVQKLKDTVKKLGESGEIKAIGELDLLFMSLRNACI 179
               SCOP domains d3dlqi_ I: Interleukin-22 (IL-22)                                                                                                            SCOP domains
               CATH domains 3dlqI00 I:40-179  [code=1.20.1250.10, no name defined]                                                                                       CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhh..hhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhh---------hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------G--------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------INTERLEUKIN_10       --------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: I:40-62 Exon 1.2  PDB: I:63-84Exon 1.3  PDB: I:85-130 UniProt: 85-132         Exon 1.4 [INCOMPLETE] Exon 1.5  PDB: I:155-179  Transcript 1
                 3dlq I  40 ARLDKSNFQQPYITNRTFMLAKEASLADNNTDVRLIGEKLFHGVSMSERCYLMKQVLNFTLEEVLFPQSDRFQPYMQEVVPFLARLSNRLS---------HIQRNVQKLKDTVKKLGESGEIKAIGELDLLFMSLRNACI 179
                                    49        59        69        79        89        99       109       119       129|        -|      149       159       169       179
                                                                                                                    130       140                                       

Chain R from PDB  Type:PROTEIN  Length:201
 aligned with I22R1_HUMAN | Q8N6P7 from UniProtKB/Swiss-Prot  Length:574

    Alignment length:209
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219         
          I22R1_HUMAN    20 DPSDLLQHVKFQSSNFENILTWDSGPEGTPDTVYSIEYKTYGERDWVAKKGCQRITRKSCNLTVETGNLTELYYARVTAVSAGGRSATKMTDRFSSLQHTTLKPPDVTCISKVRSIQMIVHPTPTPIRAGDGHRLTLEDIFHDLFYHLELQVNRTYQMHLGGKQREYEFFGLTPDTEFLGTIMICVPTWAKESAPYMCRVKTLPDRTWT 228
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhh.eeeeeeeee..eeeeeeee.......eeeeeeeee......ee..........eee.hhhhh.....eeeeeeeee....eeeee....hhhhhh......eeeee...eeeeee.........----..hhhhhh...eeeeeee.----.eeeee...eeeee......eeeeeeeeeehhhhee...eeeeee........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------P--------------------------------------------------------------------------I---S------------P------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dlq R  20 DPSDLLQHVKFQSSNFENILTWDSGPEGTPDTVYSIEYKTYGERDWVAKKGCQRITRKSCNLTVETGNLTELYYARVTAVSAGGRSATKMTDRFSSLQHTTLKPPDVTCISKVRSIQMIVHPTPTPIRA----RLTLEDIFHDLFYHLELQV----QMHLGGKQREYEFFGLTPDTEFLGTIMILVPTWAKESAPYMCRVKTLPDRTWT 228
                                    29        39        49        59        69        79        89        99       109       119       129       139        |-   |   159       169 |    |179       189       199       209       219         
                                                                                                                                                          148  153               171  176                                                    

   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  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (19, 20)

Asymmetric/Biological Unit(hide GO term definitions)
Chain I   (IL22_HUMAN | Q9GZX6)
molecular function
    GO:0005125    cytokine activity    Functions to control the survival, growth, differentiation and effector function of tissues and cells.
    GO:0045518    interleukin-22 receptor binding    Interacting selectively and non-covalently with the interleukin-22 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: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: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:0046427    positive regulation of JAK-STAT cascade    Any process that activates or increases the frequency, rate or extent of the JAK-STAT signaling pathway activity.
    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: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.

Chain R   (I22R1_HUMAN | Q8N6P7)
molecular function
    GO:0004904    interferon receptor activity    Combining with an interferon and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity.
    GO:0042015    interleukin-20 binding    Interacting selectively and non-covalently with interleukin-20.
    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:0008150    biological_process    Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
    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:0050829    defense response to Gram-negative bacterium    Reactions triggered in response to the presence of a Gram-negative bacterium that act to protect the cell or organism.
cellular component
    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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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.

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    Gln I:112 - Pro I:113   [ RasMol ]  
    Gly R:47 - Thr R:48   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        I22R1_HUMAN | Q8N6P73dgc
        IL22_HUMAN | Q9GZX61m4r 1ykb 3dgc 3g9v 3q1s

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3DLQ)