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(-) Description

Title :  INTERFERON-LAMBDA IS FUNCTIONALLY AN INTERFERON BUT STRUCTURALLY RELATED TO THE IL-10 FAMILY
 
Authors :  H. H. Gad, O. J. Hamming, Hartmann R.
Date :  15 May 09  (Deposition) - 21 Jul 09  (Release) - 11 Aug 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Interferon, Il-22, Antiviral, Antiviral Defense, Cytokine, Secreted (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. H. Gad, C. Dellgren, O. J. Hamming, S. Vends, S. R. Paludan, R. Hartmann
Interferon-{Lambda} Is Functionally An Interferon But Structurally Related To The Interleukin-10 Family
J. Biol. Chem. V. 284 20869 2009
PubMed-ID: 19457860  |  Reference-DOI: 10.1074/JBC.M109.002923
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - INTERLEUKIN-28B
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: IL28B, IFNL3, IFNL4, IL28C, ZCYTO22
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: IL-28B, IL-28C, INTERFERON LAMBDA-3, IFN-LAMBDA-3, INTERFERON LAMBDA-4, IFN-LAMBDA-4, CYTOKINE ZCYTO22

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 35)

Asymmetric Unit (1, 35)
No.NameCountTypeFull Name
1IOD35Ligand/IonIODIDE ION
Biological Unit 1 (1, 23)
No.NameCountTypeFull Name
1IOD23Ligand/IonIODIDE ION
Biological Unit 2 (1, 12)
No.NameCountTypeFull Name
1IOD12Ligand/IonIODIDE ION

(-) Sites  (28, 28)

Asymmetric Unit (28, 28)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR A:92BINDING SITE FOR RESIDUE IOD A 164
02AC2SOFTWAREARG B:101BINDING SITE FOR RESIDUE IOD A 165
03AC3SOFTWAREGLU A:29 , ARG C:41 , ARG C:45BINDING SITE FOR RESIDUE IOD A 169
04AC4SOFTWARETRP A:47 , ARG A:124BINDING SITE FOR RESIDUE IOD A 170
05AC5SOFTWAREPHE A:146BINDING SITE FOR RESIDUE IOD A 171
06AC6SOFTWAREASP A:48 , ARG A:50 , ARG A:151 , ASP A:152BINDING SITE FOR RESIDUE IOD A 172
07AC7SOFTWAREASN A:154 , SER A:158 , HOH A:186BINDING SITE FOR RESIDUE IOD A 173
08AC8SOFTWAREGLN B:88 , THR B:92BINDING SITE FOR RESIDUE IOD B 164
09AC9SOFTWARELYS B:24BINDING SITE FOR RESIDUE IOD B 165
10BC1SOFTWAREHIS B:120BINDING SITE FOR RESIDUE IOD B 167
11BC2SOFTWAREASN B:154 , SER B:158 , LEU B:161 , CYS B:162BINDING SITE FOR RESIDUE IOD B 168
12BC3SOFTWAREGLN A:105 , GLY B:111BINDING SITE FOR RESIDUE IOD B 170
13BC4SOFTWARETHR C:92BINDING SITE FOR RESIDUE IOD C 164
14BC5SOFTWAREPHE C:146BINDING SITE FOR RESIDUE IOD C 165
15BC6SOFTWAREASP C:48 , ARG C:50 , ASP C:152BINDING SITE FOR RESIDUE IOD C 166
16BC7SOFTWAREGLN C:53BINDING SITE FOR RESIDUE IOD C 167
17BC8SOFTWARELYS C:70BINDING SITE FOR RESIDUE IOD C 168
18BC9SOFTWAREARG C:2BINDING SITE FOR RESIDUE IOD C 169
19CC1SOFTWAREPRO B:112BINDING SITE FOR RESIDUE IOD C 170
20CC2SOFTWAREHIS C:91 , HIS C:95BINDING SITE FOR RESIDUE IOD C 171
21CC3SOFTWARELYS A:21BINDING SITE FOR RESIDUE IOD C 172
22CC4SOFTWAREARG A:45 , GLU C:29BINDING SITE FOR RESIDUE IOD C 173
23CC5SOFTWAREHIS C:120BINDING SITE FOR RESIDUE IOD C 174
24CC6SOFTWAREILE C:6BINDING SITE FOR RESIDUE IOD C 176
25CC7SOFTWAREGLU B:29 , ARG D:41 , ARG D:45BINDING SITE FOR RESIDUE IOD D 164
26CC8SOFTWAREPHE D:146BINDING SITE FOR RESIDUE IOD D 165
27CC9SOFTWARELYS D:70BINDING SITE FOR RESIDUE IOD D 167
28DC1SOFTWAREGLN D:88 , PRO D:89BINDING SITE FOR RESIDUE IOD D 168

(-) SS Bonds  (11, 11)

Asymmetric Unit
No.Residues
1A:4 -A:103
2A:36 -C:36
3A:38 -A:136
4A:155 -A:162
5B:4 -B:103
6B:38 -B:136
7B:155 -B:162
8C:4 -C:103
9C:38 -C:136
10C:155 -C:162
11D:38 -D:136

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Gly B:111 -Pro B:112
2Lys C:34 -Asp C:35
3Leu D:86 -Asp D:87

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 4)

Asymmetric Unit (1, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_063420K70RIFNL3_HUMANPolymorphism8103142A/B/C/DK37R
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_063420K70RIFNL3_HUMANPolymorphism8103142A/CK37R
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_063420K70RIFNL3_HUMANPolymorphism8103142B/DK37R
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3HHC)

(-) Exons   (0, 0)

(no "Exon" information available for 3HHC)

(-) 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:153
 aligned with IFNL3_HUMAN | Q8IZI9 from UniProtKB/Swiss-Prot  Length:196

    Alignment length:163
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193   
          IFNL3_HUMAN    34 ARGCHIAQFKSLSPQELQAFKRAKDALEESLLLKDCKCRSRLFPRTWDLRQLQVRERPVALEAELALTLKVLEATADTDPALGDVLDQPLHTLHHILSQLRACIQPQPTAGPRTRGRLHHWLHRLQEAPKKESPGCLEASVTFNLFRLLTRDLNCVASGDLCV 196
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhh..hhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...----------hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------R------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hhc A   1 ARGCHIAQFKSLSPQELQAFKRAKDALEESLLLKDCKCRSRLFPRTWDLRQLQVRERPVALEAELALTLKVLEATADTDPALGDVLDQPLHTLHHILSQLRACIQ----------GRLHHWLHRLQEAPKKESPGCLEASVTFNLFRLLTRDLNCVASGDLCV 163
                                    10        20        30        40        50        60        70        80        90       100    |    -     | 120       130       140       150       160   
                                                                                                                                  105        116                                               


Chain B from PDB  Type:PROTEIN  Length:157
 aligned with IFNL3_HUMAN | Q8IZI9 from UniProtKB/Swiss-Prot  Length:196

    Alignment length:160
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196
          IFNL3_HUMAN    37 CHIAQFKSLSPQELQAFKRAKDALEESLLLKDCKCRSRLFPRTWDLRQLQVRERPVALEAELALTLKVLEATADTDPALGDVLDQPLHTLHHILSQLRACIQPQPTAGPRTRGRLHHWLHRLQEAPKKESPGCLEASVTFNLFRLLTRDLNCVASGDLCV 196
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh..hhhhhhhhhhhhhhhhhhhh....................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....---..hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------R------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hhc B   4 CHIAQFKSLSPQELQAFKRAKDALEESLLLKDCKCRSRLFPRTWDLRQLQVRERPVALEAELALTLKVLEATADTDPALGDVLDQPLHTLHHILSQLRACIQP---AGPRTRGRLHHWLHRLQEAPKKESPGCLEASVTFNLFRLLTRDLNCVASGDLCV 163
                                    13        23        33        43        53        63        73        83        93       103  |   |113       123       133       143       153       163
                                                                                                                                106 110                                                     


Chain C from PDB  Type:PROTEIN  Length:151
 aligned with IFNL3_HUMAN | Q8IZI9 from UniProtKB/Swiss-Prot  Length:196

    Alignment length:162
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194  
          IFNL3_HUMAN    35 RGCHIAQFKSLSPQELQAFKRAKDALEESLLLKDCKCRSRLFPRTWDLRQLQVRERPVALEAELALTLKVLEATADTDPALGDVLDQPLHTLHHILSQLRACIQPQPTAGPRTRGRLHHWLHRLQEAPKKESPGCLEASVTFNLFRLLTRDLNCVASGDLCV 196
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhh...hhhhhhhhhhhhhhhhhhhh...............hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..-----------.hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -----------------------------------R------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3hhc C   2 RGCHIAQFKSLSPQELQAFKRAKDALEESLLLKDCKCRSRLFPRTWDLRQLQVRERPVALEAELALTLKVLEATADTDPALGDVLDQPLHTLHHILSQLRACIQ-----------RLHHWLHRLQEAPKKESPGCLEASVTFNLFRLLTRDLNCVASGDLCV 163
                                    11        21        31        41        51        61        71        81        91       101   |     -     | 121       131       141       151       161  
                                                                                                                                 105         117                                              


Chain D from PDB  Type:PROTEIN  Length:98
 aligned with IFNL3_HUMAN | Q8IZI9 from UniProtKB/Swiss-Prot  Length:196

    Alignment length:139
                                    56        66        76        86        96       106       116       126       136       146       156       166       176         
          IFNL3_HUMAN    47 PQELQAFKRAKDALEESLLLKDCKCRSRLFPRTWDLRQLQVRERPVALEAELALTLKVLEATADTDPALGDVLDQPLHTLHHILSQLRACIQPQPTAGPRTRGRLHHWLHRLQEAPKKESPGCLEASVTFNLFRLLTRD 185
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhh...................--------hhhhhhhhhhhhhhhhhh...hhhhhh...------...hhhhh..---------------------------hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -----------------------R------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hhc D  14 PQELQAFKRAKDALEESLLLKDCKCRSRLFPRTWDLRQ--------ALEAELALTLKVLEATADTDPALGDVLDQP------ILSQLRACIQ---------------------------SPGCLEASVTFNLFRLLTRD 152
                                    23        33        43       | -      | 63        73        83     |   -  |    103 |       -         -       133       143         
                                                                51       60                           89     96      105                         133
   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 3HHC)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (IFNL3_HUMAN | Q8IZI9)
molecular function
    GO:0005125    cytokine activity    Functions to control the survival, growth, differentiation and effector function of tissues and cells.
    GO:0005102    receptor binding    Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
biological process
    GO:0007259    JAK-STAT cascade    Any process in which STAT proteins (Signal Transducers and Activators of Transcription) and JAK (Janus Activated Kinase) proteins convey a signal to trigger a change in the activity or state of a cell. The JAK-STAT cascade begins with activation of STAT proteins by members of the JAK family of tyrosine kinases, proceeds through dimerization and subsequent nuclear translocation of STAT proteins, and ends with regulation of target gene expression by STAT proteins.
    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:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    GO:0045071    negative regulation of viral genome replication    Any process that stops, prevents, or reduces the frequency, rate or extent of viral genome replication.
    GO:0050778    positive regulation of immune response    Any process that activates or increases the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.
    GO:1903955    positive regulation of protein targeting to mitochondrion    Any process that activates or increases the frequency, rate or extent of protein targeting to mitochondrion.
    GO:0050863    regulation of T cell activation    Any process that modulates the frequency, rate or extent of T cell activation.
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.
    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.

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        IFNL3_HUMAN | Q8IZI9: 5t5w

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