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(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF THE HUMAN IGE-FC CEPSILON3-CEPSILON4 FRAGMENT.
 
Authors :  B. A. Wurzburg, S. C. Garman, T. S. Jardetzky
Date :  30 Aug 00  (Deposition) - 27 Sep 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Antibody, Fc, Immunoglobin Fold, "Closed" Ige-Fc, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  B. A. Wurzburg, S. C. Garman, T. S. Jardetzky
Structure Of The Human Ige-Fc C Epsilon 3-C Epsilon 4 Reveals Conformational Flexibility In The Antibody Effector Domains.
Immunity V. 13 375 2000
PubMed-ID: 11021535  |  Reference-DOI: 10.1016/S1074-7613(00)00037-6
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - IGE HEAVY CHAIN EPSILON-1
    ChainsA
    EngineeredYES
    Expression SystemTRICHOPLUSIA NI
    Expression System CommonCABBAGE LOOPER
    Expression System PlasmidPACGP67A
    Expression System Taxid7111
    Expression System Vector TypeBACULOVIRUS
    FragmentCEPSILON3-CEPSILON4
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymIGE-FC

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1FP5)

(-) Sites  (0, 0)

(no "Site" information available for 1FP5)

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:358 -A:418
2A:464 -A:524

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Met A:470 -Pro A:471
2Ser A:532 -Pro A:533

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_003885W359LIGHE_HUMANPolymorphism  ---AW478L

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_003885W359LIGHE_HUMANPolymorphism  ---AW478L

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1IG_MHCPS00290 Immunoglobulins and major histocompatibility complex proteins signature.IGHE_HUMAN83-89
297-303
403-409
  2-
A:416-422
A:522-528
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1IG_MHCPS00290 Immunoglobulins and major histocompatibility complex proteins signature.IGHE_HUMAN83-89
297-303
403-409
  4-
A:416-422
A:522-528

(-) Exons   (2, 2)

Asymmetric Unit (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003905411ENSE00001935719chr14:106068065-106067756310IGHE_HUMAN1-1041040--
1.2ENST000003905412ENSE00001508179chr14:106067548-106067228321IGHE_HUMAN104-2111080--
1.3ENST000003905413ENSE00001508174chr14:106067141-106066818324IGHE_HUMAN211-3191091A:336-438103
1.4ENST000003905414ENSE00001943927chr14:106066734-106066278457IGHE_HUMAN319-4281101A:438-543106

(-) 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:208
 aligned with IGHE_HUMAN | P01854 from UniProtKB/Swiss-Prot  Length:428

    Alignment length:208
                                   226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416        
           IGHE_HUMAN   217 VSAYLSRPSPFDLFIRKSPTITCLVVDLAPSKGTVNLTWSRASGKPVNHSTRKEEKQRNGTLTVTSTLPVGTRDWIEGETYQCRVTHPHLPRALMRSTTKTSGPRAAPEVYAFATPEWPGSRDKRTLACLIQNFMPEDISVQWLHNEVQLPDARHSTTQPRKTKGSGFFVFSRLEVTRAEWEQKDEFICRAVHEAASPSQTVQRAVSV 424
               SCOP domains d1fp5a1 A:336-438 Immunoglobulin heavy chain epsilon constant domain 3, CH3-epsilon                    d1fp5a2 A:439-543 Immunoglobulin heavy chain epsilon constant domain 4, CH4-epsilon                       SCOP domains
               CATH domains 1fp5A01 A:336-435 Immunoglobulins                                                                   1fp5A02 A:436-543 Immunoglobulins                                                                            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhhhh....eeeeeeee........eeeeee.........eeeeeee...eeeeeeeee.hhhhhhh...eeeeee.......eeeee..........eeeeee..........eeeeeeeeee.....eeeeee..ee.hhh.eee...ee.....eeeeeeeeehhhhhhhhh.eeeeee........eeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------L----------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------IG_MHC ---------------------------------------------------------------------------------------------------IG_MHC --------------- PROSITE
           Transcript 1 (1) Exon 1.3  PDB: A:336-438 UniProt: 211-319 [INCOMPLETE]                                                 --------------------------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------------------------------Exon 1.4  PDB: A:438-543 UniProt: 319-428 [INCOMPLETE]                                                     Transcript 1 (2)
                 1fp5 A 336 VSAYLSRPSPFDLFIRKSPTITCLVVDLAPSKGTVNLTWSRASGKPVNHSTRKEEKQRNGTLTVTSTLPVGTRDWIEGETYQCRVTHPHLPRALMRSTTKTSGPRAAPEVYAFATPEWPGSRDKRTLACLIQNFMPEDISVQWLHNEVQLPDARHSTTQPRKTKGSGFFVFSRLEVTRAEWEQKDEFICRAVHEAASPSQTVQRAVSV 543
                                   345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535        

   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  (2, 2)

Asymmetric Unit

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1FP5)

(-) Gene Ontology  (15, 15)

Asymmetric Unit(hide GO term definitions)
Chain A   (IGHE_HUMAN | P01854)
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:0034987    immunoglobulin receptor binding    Interacting selectively and non-covalently with one or more specific sites on an immunoglobulin receptor molecule.
biological process
    GO:0050853    B cell receptor signaling pathway    A series of molecular signals initiated by the cross-linking of an antigen receptor on a B cell.
    GO:0038095    Fc-epsilon receptor signaling pathway    A series of molecular signals initiated by the binding of the Fc portion of immunoglobulin E (IgE) to an Fc-epsilon receptor on the surface of a signal-receiving cell, and ending with regulation of a downstream cellular process, e.g. transcription. The Fc portion of an immunoglobulin is its C-terminal constant region.
    GO:0006958    complement activation, classical pathway    Any process involved in the activation of any of the steps of the classical pathway of the complement cascade which allows for the direct killing of microbes, the disposal of immune complexes, and the regulation of other immune processes.
    GO:0042742    defense response to bacterium    Reactions triggered in response to the presence of a bacterium 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:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    GO:0006911    phagocytosis, engulfment    The internalization of bacteria, immune complexes and other particulate matter or of an apoptotic cell by phagocytosis, including the membrane and cytoskeletal processes required, which involves one of three mechanisms: zippering of pseudopods around a target via repeated receptor-ligand interactions, sinking of the target directly into plasma membrane of the phagocytosing cell, or induced uptake via an enhanced membrane ruffling of the phagocytosing cell similar to macropinocytosis.
    GO:0006910    phagocytosis, recognition    The initial step in phagocytosis involving adhesion to bacteria, immune complexes and other particulate matter, or an apoptotic cell and based on recognition of factors such as bacterial cell wall components, opsonins like complement and antibody or protein receptors and lipids like phosphatidyl serine, and leading to intracellular signaling in the phagocytosing cell.
    GO:0050871    positive regulation of B cell activation    Any process that activates or increases the frequency, rate or extent of B cell activation.
cellular component
    GO:0072562    blood microparticle    A phospholipid microvesicle that is derived from any of several cell types, such as platelets, blood cells, endothelial cells, or others, and contains membrane receptors as well as other proteins characteristic of the parental cell. Microparticles are heterogeneous in size, and are characterized as microvesicles free of nucleic acids.
    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:0042571    immunoglobulin complex, circulating    An immunoglobulin complex that is secreted into extracellular space and found in mucosal areas or other tissues or circulating in the blood or lymph. In its canonical form, a circulating immunoglobulin complex is composed of two identical heavy chains and two identical light chains, held together by disulfide bonds. Some forms of are polymers of the basic structure and contain additional components such as J-chain and the secretory component.

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    Met A:470 - Pro A:471   [ RasMol ]  
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 Related Entries

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

UniProtKB/Swiss-Prot
        IGHE_HUMAN | P018541f6a 1g84 1ige 1o0v 2ige 2wqr 2y7q 3h9y 3h9z 3ha0 4ezm 4gko 4grg 4gt7 4j4p 4ki1 5anm 5hys 5lgj 5lgk

(-) Related Entries Specified in the PDB File

1f6a 1F6A CONTAINS THE SAME FC PROTEIN IN COMPLEX WITH ITS HIGH AFFINITY RECEPTOR, THE FC EPSILON RI ALPHA (SOLUBLE ECTODOMAIN).