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(-) Description

Title :  CRYSTAL STRUCTURE OF THE UNLIGANDED HUMAN INTERLEUKIN-7 RECEPTOR EXTRACELLULAR DOMAIN
 
Authors :  C. A. Mcelroy, P. J. Holland, S. T. R. Walsh
Date :  17 Nov 11  (Deposition) - 08 Feb 12  (Release) - 22 Aug 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Cytokine Receptor, Fibronectin Type 3 Fold, Membrane And Soluble, Glycosylation, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. A. Mcelroy, P. J. Holland, P. Zhao, J. M. Lim, L. Wells, E. Eisenstein S. T. Walsh
Structural Reorganization Of The Interleukin-7 Signaling Complex.
Proc. Natl. Acad. Sci. Usa V. 109 2503 2012
PubMed-ID: 22308406  |  Reference-DOI: 10.1073/PNAS.1116582109

(-) Compounds

Molecule 1 - INTERLEUKIN-7 RECEPTOR SUBUNIT ALPHA
    ChainsA, B
    EngineeredYES
    Expression SystemDROSOPHILA
    Expression System PlasmidPMT-BIPA
    Expression System StrainSCHNEIDER S2 INSECT CELLS
    Expression System Taxid32281
    Expression System Vector TypePLASMID
    GeneIL7R
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymIL-7 RECEPTOR SUBUNIT ALPHA, IL-7R SUBUNIT ALPHA, IL-7R- ALPHA, IL-7RA, CDW127

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 16)

Asymmetric/Biological Unit (5, 16)
No.NameCountTypeFull Name
1FUC2Ligand/IonALPHA-L-FUCOSE
2GOL4Ligand/IonGLYCEROL
3NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
4NGA1Ligand/IonN-ACETYL-D-GALACTOSAMINE
5SO45Ligand/IonSULFATE ION

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:131 , NAG A:902 , FUC A:903 , ARG B:207BINDING SITE FOR RESIDUE NAG A 901
02AC2SOFTWARENAG A:901 , FUC A:903BINDING SITE FOR RESIDUE NAG A 902
03AC3SOFTWARENAG A:901 , NAG A:902 , LYS B:153BINDING SITE FOR RESIDUE FUC A 903
04AC4SOFTWAREGLN A:25 , GLU A:110 , ALA A:111 , HOH A:1005 , HOH A:1049BINDING SITE FOR RESIDUE SO4 A 904
05AC5SOFTWAREGLN A:32 , THR A:76 , LYS A:77 , LYS A:78 , HOH A:1026BINDING SITE FOR RESIDUE SO4 A 905
06AC6SOFTWAREVAL A:127 , LYS A:167 , PRO B:209BINDING SITE FOR RESIDUE GOL A 906
07AC7SOFTWAREPHE B:113 , ASN B:131 , NAG B:302 , FUC B:303BINDING SITE FOR RESIDUE NAG B 301
08AC8SOFTWARENAG B:301 , FUC B:303BINDING SITE FOR RESIDUE NAG B 302
09AC9SOFTWAREASP B:114 , NAG B:301 , NAG B:302BINDING SITE FOR RESIDUE FUC B 303
10BC1SOFTWARELEU B:26 , PRO B:109 , GLU B:110 , SER B:133 , LEU B:135 , GLN B:136 , TYR B:139 , VAL B:142 , LEU B:143 , HOH B:406 , HOH B:438 , HOH B:459BINDING SITE FOR RESIDUE NGA B 304
11BC2SOFTWARELEU B:163 , SER B:164 , SER B:165BINDING SITE FOR RESIDUE SO4 B 305
12BC3SOFTWAREVAL B:60 , LYS B:61 , CYS B:62BINDING SITE FOR RESIDUE SO4 B 306
13BC4SOFTWAREGLN B:32 , THR B:76 , LYS B:77 , LYS B:78BINDING SITE FOR RESIDUE SO4 B 307
14BC5SOFTWAREALA B:56 , LEU B:57BINDING SITE FOR RESIDUE GOL B 308
15BC6SOFTWARELYS A:94 , ASN B:64 , ARG B:66BINDING SITE FOR RESIDUE GOL B 309
16BC7SOFTWAREPRO B:202 , SER B:203BINDING SITE FOR RESIDUE GOL B 310

(-) SS Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1A:22 -A:37
2A:54 -A:62
3A:88 -A:98
4B:22 -B:37
5B:54 -B:62
6B:88 -B:98

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3UP1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (4, 8)

Asymmetric/Biological Unit (4, 8)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_021286T66IIL7RA_HUMANDisease (T(-)1494558A/BT46I
2UniProtVAR_021287E113DIL7RA_HUMANPolymorphism11567735A/BE93D
3UniProtVAR_034870P132SIL7RA_HUMANDisease (T(-)  ---A/BP112S
4UniProtVAR_021288I138VIL7RA_HUMANDisease (T(-)1494555A/BV118V

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

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FN3PS50853 Fibronectin type-III domain profile.IL7RA_HUMAN131-231
 
  2A:111-211
B:111-211
2HEMATOPO_REC_S_F1PS01355 Short hematopoietin receptor family 1 signature.IL7RA_HUMAN195-226
 
  2A:175-206
B:175-206

(-) Exons   (0, 0)

(no "Exon" information available for 3UP1)

(-) 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 A from PDB  Type:PROTEIN  Length:201
 aligned with IL7RA_HUMAN | P16871 from UniProtKB/Swiss-Prot  Length:459

    Alignment length:201
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231 
          IL7RA_HUMAN    32 DAELDDYSFSCYSQLEVNGSQHSLTCAFEDPDVNTTNLEFEICGALVEVKCLNFRKLQEIYFIETKKFLLIGKSNICVKVGEKSLTCKKIDLTTIVKPEAPFDLSVIYREGANDFVVTFNTSHLQKKYVKVLMHDVAYRQEKDENKWTHVNLSSTKLTLLQRKLQPAAMYEIKVRSIPDHYFKGFWSEWSPSYYFRTPEIN 232
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh.eeeeeeeeee..eeeeeeee.........eeeeee.......eee.eee..eeeeee.......eeeeeeee..eeeeeeeee.hhh......eeeeeeee....eeeeeeehhhhhh.....eeeeeeeee.......eeeee...eeeee.hhh....eeeeeeeeee..............eeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------I----------------------------------------------D------------------S-----V---------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------------------------------------------------------------------------------------------------FN3  PDB: A:111-211 UniProt: 131-231                                                                 - PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------HEMATOPO_REC_S_F1  PDB: A:175-20------ PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3up1 A  12 DAELDDYSFSCYSQLEVNGSQHSLTCAFEDPDVNTTNLEFEICGALVEVKCLNFRKLQEIYFIETKKFLLIGKSNICVKVGEKSLTCKKIDLTTIVKPEAPFDLSVVYREGANDFVVTFNTSHLQKKYVKVLMHDVAYRQEKDENKWTHVNLSSTKLTLLQRKLQPAAMYEIKVRSIPDHYFKGFWSEWSPSYYFRTPEIN 212
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211 

Chain B from PDB  Type:PROTEIN  Length:196
 aligned with IL7RA_HUMAN | P16871 from UniProtKB/Swiss-Prot  Length:459

    Alignment length:196
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225      
          IL7RA_HUMAN    36 DDYSFSCYSQLEVNGSQHSLTCAFEDPDVNTTNLEFEICGALVEVKCLNFRKLQEIYFIETKKFLLIGKSNICVKVGEKSLTCKKIDLTTIVKPEAPFDLSVIYREGANDFVVTFNTSHLQKKYVKVLMHDVAYRQEKDENKWTHVNLSSTKLTLLQRKLQPAAMYEIKVRSIPDHYFKGFWSEWSPSYYFRTPEI 231
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeee..eeeeeeee..........eeeee.......eee.eee..eeeeee........eeeeeee..eeeeeeeehhhhh......eeeeeeee....eeeeeee..hhhhhh...eeeeeeeee.......eeeee...eeeee.hhh....eeeeeeeeee..............eeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------I----------------------------------------------D------------------S-----V--------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------------------------------------------------------------------------------------------FN3  PDB: B:111-211 UniProt: 131-231                                                                  PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------HEMATOPO_REC_S_F1  PDB: B:175-20----- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3up1 B  16 DDYSFSCYSQLEVNGSQHSLTCAFEDPDVNTTNLEFEICGALVEVKCLNFRKLQEIYFIETKKFLLIGKSNICVKVGEKSLTCKKIDLTTIVKPEAPFDLSVVYREGANDFVVTFNTSHLQKKYVKVLMHDVAYRQEKDENKWTHVNLSSTKLTLLQRKLQPAAMYEIKVRSIPDHYFKGFWSEWSPSYYFRTPEI 211
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205      

   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 3UP1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3UP1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3UP1)

(-) Gene Ontology  (26, 26)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (IL7RA_HUMAN | P16871)
molecular function
    GO:0003823    antigen binding    Interacting selectively and non-covalently with an antigen, any substance which is capable of inducing a specific immune response and of reacting with the products of that response, the specific antibody or specifically sensitized T-lymphocytes, or both. Binding may counteract the biological activity of the antigen.
    GO:0004896    cytokine receptor activity    Combining with a cytokine and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity.
    GO:0004917    interleukin-7 receptor activity    Combining with interleukin-7 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).
biological process
    GO:0042100    B cell proliferation    The expansion of a B cell population by cell division. Follows B cell activation.
    GO:0030217    T cell differentiation    The process in which a precursor cell type acquires characteristics of a more mature T-cell. A T cell is a type of lymphocyte whose definin characteristic is the expression of a T cell receptor complex.
    GO:0016049    cell growth    The process in which a cell irreversibly increases in size over time by accretion and biosynthetic production of matter similar to that already present.
    GO:0000902    cell morphogenesis    The developmental process in which the size or shape of a cell is generated and organized.
    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: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:0048872    homeostasis of number of cells    Any biological process involved in the maintenance of the steady-state number of cells within a population of cells.
    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:0002377    immunoglobulin production    The appearance of immunoglobulin due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
    GO:0038111    interleukin-7-mediated signaling pathway    A series of molecular signals initiated by the binding of interleukin-7 to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0048535    lymph node development    The process whose specific outcome is the progression of lymph nodes over time, from their formation to the mature structure. A lymph node is a round, oval, or bean shaped structure localized in clusters along the lymphatic vessels, with a distinct internal structure including specialized vasculature and B- and T-zones for the activation of lymphocytes.
    GO:0001915    negative regulation of T cell mediated cytotoxicity    Any process that stops, prevents, or reduces the rate of T cell mediated cytotoxicity.
    GO:0033089    positive regulation of T cell differentiation in thymus    Any process that activates or increases the frequency, rate or extent of T cell differentiation in the thymus.
    GO:0010628    positive regulation of gene expression    Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:0000018    regulation of DNA recombination    Any process that modulates the frequency, rate or extent of DNA recombination, a DNA metabolic process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents.
    GO:0008361    regulation of cell size    Any process that modulates the size of a cell.
    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:0009897    external side of plasma membrane    The leaflet of the plasma membrane that faces away from the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
    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: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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 Related Entries

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        IL7RA_HUMAN | P168713di2 3di3 5j11

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