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(-) Description

Title :  D2 DOMAIN OF HUMAN IFNAR2
 
Authors :  C. Thomas, K. C. Garcia
Date :  31 May 11  (Deposition) - 31 Aug 11  (Release) - 21 Mar 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Human, Type I Interferons, Receptor Chain, Ifnar2, Fibronectin Type Iii Module, Part Of Type I Interferon Receptor Chain, Interferon, Extracellular Space, Signaling Protein Receptor (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Thomas, I. Moraga, D. Levin, P. O. Krutzik, Y. Podoplelova, A. Trejo C. Lee, G. Yarden, S. E. Vleck, J. S. Glenn, G. P. Nolan, J. Piehler, G. Schreiber, K. C. Garcia
Structural Linkage Between Ligand Discrimination And Receptor Activation By Type I Interferons.
Cell(Cambridge, Mass. ) V. 146 621 2011
PubMed-ID: 21854986  |  Reference-DOI: 10.1016/J.CELL.2011.06.048

(-) Compounds

Molecule 1 - INTERFERON ALPHA/BETA RECEPTOR 2
    ChainsA, B, C
    EngineeredYES
    Expression SystemTRICHOPLUSIA NI
    Expression System Taxid7111
    FragmentUNP RESIDUES 131-232
    GeneIFNAR2, IFNABR, IFNARB
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymIFN-R-2, IFN-ALPHA BINDING PROTEIN, IFN-ALPHA/BETA RECEPTOR 2, INTERFERON ALPHA BINDING PROTEIN, TYPE I INTERFERON RECEPTOR 2

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit ABC
Biological Unit 1 (1x)A  
Biological Unit 2 (1x) B 
Biological Unit 3 (1x)  C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2MSE4Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MSE1Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MSE1Mod. Amino AcidSELENOMETHIONINE
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MSE2Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:172BINDING SITE FOR RESIDUE CL A 1
2AC2SOFTWARETHR A:167BINDING SITE FOR RESIDUE CL C 1

(-) SS Bonds  (3, 3)

Asymmetric Unit
No.Residues
1A:180 -A:200
2B:180 -B:200
3C:180 -C:200

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3S8W)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 3)

Asymmetric Unit (1, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_020523I196VINAR2_HUMANPolymorphism17860223A/B/CI169V

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_020523I196VINAR2_HUMANPolymorphism17860223AI169V

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_020523I196VINAR2_HUMANPolymorphism17860223BI169V

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 3 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_020523I196VINAR2_HUMANPolymorphism17860223CI169V

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3S8W)

(-) Exons   (2, 6)

Asymmetric Unit (2, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1dENST000003421361dENSE00001384199chr21:34602279-34602521243INAR2_HUMAN-00--
1.3aENST000003421363aENSE00001366893chr21:34614145-34614282138INAR2_HUMAN1-19190--
1.4ENST000003421364ENSE00001043262chr21:34615978-3461601942INAR2_HUMAN19-33150--
1.5ENST000003421365ENSE00001784597chr21:34617256-34617379124INAR2_HUMAN33-74420--
1.7bENST000003421367bENSE00001733110chr21:34619023-34619195173INAR2_HUMAN74-132590--
1.8aENST000003421368aENSE00002144798chr21:34621014-34621159146INAR2_HUMAN132-180493A:106-153 (gaps)
B:107-153 (gaps)
C:106-153 (gaps)
48
47
48
1.10ENST0000034213610ENSE00002186976chr21:34624967-34625135169INAR2_HUMAN181-237573A:154-205 (gaps)
B:154-205 (gaps)
C:154-205
52
52
52
1.11ENST0000034213611ENSE00001781920chr21:34632902-34633032131INAR2_HUMAN237-280440--
1.12gENST0000034213612gENSE00001764722chr21:34635098-346368301733INAR2_HUMAN281-5152350--

(-) 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:77
 aligned with INAR2_HUMAN | P48551 from UniProtKB/Swiss-Prot  Length:515

    Alignment length:100
                                   142       152       162       172       182       192       202       212       222       232
          INAR2_HUMAN   133 SFEPPEFEIVGFTNHINVMVKFPSIVEEELQFDLSLVIEEQSEGIVKKHKPEIKGNMSGNFTYIIDKLIPNTNYCVSVYLEHSDEQAVIKSPLKCTLLPP 232
               SCOP domains ---------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee....eeeeee.------------.eeeeee....eeee....------.eeeee.......eeeeeeee..-----......eeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------V------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.8a  PDB: A:106-153 (gaps) [INCOMPLETE]   Exon 1.10  PDB: A:154-205 (gaps) UniProt: 181-237    Transcript 1
                 3s8w A 106 SFEPPEFEIVGFTNHINVmVKF------------SLVIEEQSEGIVKKHKPEI------NFTYIIDKLIPNTNYCVSVYLEH-----VIKSPLKCTLLPP 205
                                   115       125 |       -    |  145       155  |    165       175       185 |     195       205
                                            124-MSE         140               158    165                   187   193            
                                               127                                                                              

Chain B from PDB  Type:PROTEIN  Length:81
 aligned with INAR2_HUMAN | P48551 from UniProtKB/Swiss-Prot  Length:515

    Alignment length:99
                                   143       153       163       173       183       193       203       213       223         
          INAR2_HUMAN   134 FEPPEFEIVGFTNHINVMVKFPSIVEEELQFDLSLVIEEQSEGIVKKHKPEIKGNMSGNFTYIIDKLIPNTNYCVSVYLEHSDEQAVIKSPLKCTLLPP 232
               SCOP domains --------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee....eeeeee.-----------.eeeeeeee..eeeee....------.eeeee.......eeeeeeeee...-.......eeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------V------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.8a  PDB: B:107-153 (gaps) [INCOMPLETE]  Exon 1.10  PDB: B:154-205 (gaps) UniProt: 181-237    Transcript 1
                 3s8w B 107 FEPPEFEIVGFTNHINVmVKF-----------LSLVIEEQSEGIVKKHKPEI------NFTYIIDKLIPNTNYCVSVYLEHSD-QAVIKSPLKCTLLPP 205
                                   116       126|        -  |    146       156 |     166       176       186  | |  196         
                                           124-MSE        139                158    165                     189 |              
                                              127                                                             191              

Chain C from PDB  Type:PROTEIN  Length:92
 aligned with INAR2_HUMAN | P48551 from UniProtKB/Swiss-Prot  Length:515

    Alignment length:100
                                   142       152       162       172       182       192       202       212       222       232
          INAR2_HUMAN   133 SFEPPEFEIVGFTNHINVMVKFPSIVEEELQFDLSLVIEEQSEGIVKKHKPEIKGNMSGNFTYIIDKLIPNTNYCVSVYLEHSDEQAVIKSPLKCTLLPP 232
               SCOP domains ---------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee....eeeeeee.--------...eeeeeeee..eeeee..ee.....eeeeeee.......eeeeeeeee............eeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------V------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.8a  PDB: C:106-153 (gaps) [INCOMPLETE]   Exon 1.10  PDB: C:154-205 UniProt: 181-237           Transcript 1
                 3s8w C 106 SFEPPEFEIVGFTNHINVmVKFP--------FDLSLVIEEQSEGIVKKHKPEIKGNmSGNFTYIIDKLIPNTNYCVSVYLEHSDEQAVIKSPLKCTLLPP 205
                                   115       125  |      - |     145       155      |165       175       185       195       205
                                            124-MSE      137                      162-MSE                                       

   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 3S8W)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3S8W)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3S8W)

(-) Gene Ontology  (20, 20)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (INAR2_HUMAN | P48551)
molecular function
    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).
    GO:0019901    protein kinase binding    Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
    GO:0019962    type I interferon binding    Interacting selectively and non-covalently with a type I interferon. Type I interferons include the interferon-alpha, beta, delta, epsilon, zeta, kappa, tau, and omega gene families.
    GO:0004905    type I interferon receptor activity    Combining with a type I interferon and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity. Type I interferons include the interferon-alpha, beta, delta, epsilon, zeta, kappa, tau, and omega gene families.
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:0008283    cell proliferation    The multiplication or reproduction of cells, resulting in the expansion of a cell population.
    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:0006357    regulation of transcription from RNA polymerase II promoter    Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0060338    regulation of type I interferon-mediated signaling pathway    Any process that modulates the rate, frequency or extent of a type I interferon-mediated signaling pathway. A type I interferon-mediated signaling pathway is the series of molecular events generated as a consequence of a type I interferon binding to a cell surface receptor.
    GO:0035455    response to interferon-alpha    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 interferon-alpha stimulus. Interferon-alpha is a type I interferon.
    GO:0009615    response to virus    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 stimulus from a virus.
    GO:0060337    type I interferon signaling pathway    A series of molecular signals initiated by the binding of a type I interferon to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families.
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: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: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: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
        INAR2_HUMAN | P485511n6u 1n6v 2hym 2kz1 2lag 3s9d 3se3 3se4

(-) Related Entries Specified in the PDB File

3s98 3s9d