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(-) Description

Title :  STRUCTURE OF THE IL-10R2 COMMON CHAIN
 
Authors :  S. I. Yoon, M. R. Walter
Date :  09 Feb 10  (Deposition) - 26 May 10  (Release) - 09 Jun 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.14
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Il-10R2, Receptor, Common Chain, Cytokine, Il-10, Il-22, Il-26, Il- 28, Il-29, Disulfide Bond, Glycoprotein, Membrane, Phosphoprotein, Polymorphism, Transmembrane, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. I. Yoon, B. C. Jones, N. J. Logsdon, B. D. Harris, A. Deshpande, S. Radaeva, B. A. Halloran, B. Gao, M. R. Walter
Structure And Mechanism Of Receptor Sharing By The Il-10R2 Common Chain.
Structure V. 18 638 2010
PubMed-ID: 20462497  |  Reference-DOI: 10.1016/J.STR.2010.02.009

(-) Compounds

Molecule 1 - INTERLEUKIN-10 RECEPTOR SUBUNIT BETA
    ChainsA, B
    FragmentEXTRACELLULAR DOMAIN
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymIL-10 RECEPTOR SUBUNIT BETA, IL-10R SUBUNIT BETA, IL-10RB, INTERLEUKIN-10 RECEPTOR SUBUNIT 2, IL-10R SUBUNIT 2, IL-10R2, CYTOKINE RECEPTOR FAMILY 2 MEMBER 4, CRF2-4, CYTOKINE RECEPTOR CLASS- II MEMBER 4

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 11)

Asymmetric Unit (2, 11)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2SO410Ligand/IonSULFATE ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2SO43Ligand/IonSULFATE ION
Biological Unit 2 (1, 7)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2SO47Ligand/IonSULFATE ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETRP A:159 , GLN A:161 , GLY A:162 , THR A:163BINDING SITE FOR RESIDUE SO4 A 604
02AC2SOFTWARETRP A:184 , THR A:185 , THR A:186 , GLN A:211BINDING SITE FOR RESIDUE SO4 A 606
03AC3SOFTWAREARG A:90 , HIS A:97 , HOH A:242BINDING SITE FOR RESIDUE SO4 A 608
04AC4SOFTWAREPRO A:171 , GLN A:172 , TYR A:173 , PHE A:175 , GLU A:176 , HOH A:258 , HOH A:262 , GLU B:139 , TYR B:140BINDING SITE FOR RESIDUE GOL A 701
05AC5SOFTWARETYR B:82 , VAL B:148 , TYR B:149 , ASN B:150 , SER B:151 , ARG B:198 , HOH B:294BINDING SITE FOR RESIDUE SO4 B 601
06AC6SOFTWARESER B:80 , LYS B:81 , TYR B:82 , HOH B:279BINDING SITE FOR RESIDUE SO4 B 602
07AC7SOFTWARETRP B:159 , GLY B:162 , CYS B:188 , HOH B:307BINDING SITE FOR RESIDUE SO4 B 605
08AC8SOFTWARETRP B:184 , THR B:185 , THR B:186 , GLN B:211BINDING SITE FOR RESIDUE SO4 B 607
09AC9SOFTWAREARG B:90BINDING SITE FOR RESIDUE SO4 B 609
10BC1SOFTWARELYS A:47 , GLU B:25 , ASN B:26BINDING SITE FOR RESIDUE SO4 B 610
11BC2SOFTWAREARG B:88 , TRP B:100BINDING SITE FOR RESIDUE SO4 B 611

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:66 -A:74
2A:188 -A:209
3B:66 -B:74
4B:188 -B:209

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3LQM)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 2)

Asymmetric Unit (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_020666K47EI10R2_HUMANPolymorphism2834167A/BK47E

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_020666K47EI10R2_HUMANPolymorphism2834167AK47E

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_020666K47EI10R2_HUMANPolymorphism2834167BK47E

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

(-) PROSITE Motifs  (1, 4)

Asymmetric Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FN3PS50853 Fibronectin type-III domain profile.I10R2_HUMAN23-111
 
114-216
 
  4A:23-111
B:23-111
A:114-216
B:114-215
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FN3PS50853 Fibronectin type-III domain profile.I10R2_HUMAN23-111
 
114-216
 
  2A:23-111
-
A:114-216
-
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FN3PS50853 Fibronectin type-III domain profile.I10R2_HUMAN23-111
 
114-216
 
  2-
B:23-111
-
B:114-215

(-) Exons   (0, 0)

(no "Exon" information available for 3LQM)

(-) 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:201
 aligned with I10R2_HUMAN | Q08334 from UniProtKB/Swiss-Prot  Length:325

    Alignment length:201
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219 
          I10R2_HUMAN    20 MVPPPENVRMNSVNFKNILQWESPAFAKGNLTFTAQYLSYRIFQDKCMNTTLTECDFSSLSKYGDHTLRVRAEFADEHSDWVNITFCPVDDTIIGPPGMQVEVLADSLHMRFLAPKIENEYETWTMKNVYNSWTYNVQYWKNGTDEKFQITPQYDFEVLRNLEPWTTYCVQVRGFLPDRNKAGEWSEPVCEQTTHDETVPS 220
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeee..eeeeeee.........eeeeeeee..eeeeeeeee...eee.........eeeeeeeee..ee...eeeeehhhhhh.....eeeeeee..eeeeeee..eee....eeehhhhh...eeeeeeee......eee.....eeee.......eeeeeeeee.............eeee..hhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------E----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---FN3  PDB: A:23-111 UniProt: 23-111                                                       --FN3  PDB: A:114-216 UniProt: 114-216                                                                   ---- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lqm A  20 MVPPPENVRMNSVNFKNILQWESPAFAKGQLTFTAQYLSYRIFQDKCMQTTLTECDFSSLSKYGDHTLRVRAEFADEHSDWVQITFSPVDDTIIGPPGMQVEVLADCLHMRFLAPKIENEYETWTMKNVYNSWTYNVQYWKQGTDEKFQITPQYDFEVLRNLEPWTTYCVQVRGFLPDRNKAGEWSEPVCEQTTHDETVPS 220
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219 

Chain B from PDB  Type:PROTEIN  Length:196
 aligned with I10R2_HUMAN | Q08334 from UniProtKB/Swiss-Prot  Length:325

    Alignment length:196
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209      
          I10R2_HUMAN    20 MVPPPENVRMNSVNFKNILQWESPAFAKGNLTFTAQYLSYRIFQDKCMNTTLTECDFSSLSKYGDHTLRVRAEFADEHSDWVNITFCPVDDTIIGPPGMQVEVLADSLHMRFLAPKIENEYETWTMKNVYNSWTYNVQYWKNGTDEKFQITPQYDFEVLRNLEPWTTYCVQVRGFLPDRNKAGEWSEPVCEQTTHD 215
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Tissue_fac-3lqmB03 B:20-100                                                      ----------Interfer-bind-3lqmB01 B:111-213                                                                        -- Pfam domains (1)
           Pfam domains (2) Tissue_fac-3lqmB04 B:20-100                                                      ----------Interfer-bind-3lqmB02 B:111-213                                                                        -- Pfam domains (2)
         Sec.struct. author .....eeeeeeee..eeeeeee.........eeeeeeee..eeeeeeeee...eee.........eeeeeeeee..ee...eeeeehhhhhh.....eeeeee....eeeeee...........hhhhhh...eeeeeeee.....eeee.....eeee.......eeeeeeeeeehhhhee......eeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------E------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---FN3  PDB: B:23-111 UniProt: 23-111                                                       --FN3  PDB: B:114-215 UniProt: 114-216                                                                   PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lqm B  20 MVPPPENVRMNSVNFKNILQWESPAFAKGQLTFTAQYLSYRIFQDKCMQTTLTECDFSSLSKYGDHTLRVRAEFADEHSDWVQITFSPVDDTIIGPPGMQVEVLADCLHMRFLAPKIENEYETWTMKNVYNSWTYNVQYWKQGTDEKFQITPQYDFEVLRNLEPWTTYCVQVRGFLPDRNKAGEWSEPVCEQTTHD 215
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209      

   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  (0, 0)

(no "SCOP Domain" information available for 3LQM)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3LQM)

(-) Pfam Domains  (2, 4)

Asymmetric Unit
(-)
Clan: E-set (290)

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (I10R2_HUMAN | Q08334)
molecular function
    GO:0004920    interleukin-10 receptor activity    Combining with interleukin-10 and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity.
    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:0004872    receptor activity    Combining with an extracellular or intracellular messenger to initiate a change in cell activity.
biological process
    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:0051607    defense response to virus    Reactions triggered in response to the presence of a virus that act to protect the cell or organism.
    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: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: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: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:0032002    interleukin-28 receptor complex    A protein complex that binds interleukin-28 and interleukin-29. It is composed of an alpha and a beta receptor subunit (in human IFNLR1/IL28Ralpha & IL10RB) and either Interleukin-28 (IFNL2 or IFNL3) or Interleukin-29 (IFNL1).
    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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 Related Entries

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

UniProtKB/Swiss-Prot
        I10R2_HUMAN | Q083345t5w

(-) Related Entries Specified in the PDB File

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