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(-) Description

Title :  THE CRYSTAL STRUCTURE OF IGE FC REVEALS AN ASYMMETRICALLY BENT CONFORMATION
 
Authors :  T. Wan, R. L. Beavil, S. M. Fabiane, A. J. Beavil, M. K. Sohi, M. Keown, R. J A. J. Henry, R. J. Owens, H. J. Gould, B. J. Sutton
Date :  06 Sep 02  (Deposition) - 18 Sep 02  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ige Fc, Immunoglobulin E, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Wan, R. L. Beavil, S. M. Fabiane, A. J. Beavil, M. K. Sohi, M. Keown, R. J. Young, A. J. Henry, R. J. Owens, H. J. Gould, B. J. Sutton
The Crystal Structure Of Ige Fc Reveals An Asymmetrically Bent Conformation
Nat. Immunol. V. 3 681 2002
PubMed-ID: 12068291  |  Reference-DOI: 10.1038/NI811

(-) Compounds

Molecule 1 - IMMUNOGLOBULIN HEAVY CHAIN EPSILON-1
    Chains: A, B
    Engineered: YES
    Expression System: MUS MUSCULUS
    Expression System Cell Line: MOUSE MYELOMA NS0
    Expression System Common: HOUSE MOUSE
    Expression System Taxid: 10090
    Expression System Vector: PEE6
    Expression System Vector Type: EUKARYOTIC
    Fragment: FC PORTION, RESIDUES 251-573
    Gene: IGE(ND)
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: IGE FC

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 20)

Asymmetric/Biological Unit (5, 20)
No.NameCountTypeFull Name
1BMA3Ligand/IonBETA-D-MANNOSE
2GOL2Ligand/IonGLYCEROL
3MAN7Ligand/IonALPHA-D-MANNOSE
4NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
5SO44Ligand/IonSULFATE ION

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
No.NameEvidenceResiduesDescription
01AC1SOFTWARENAG A:2 , ASP A:362 , GLN A:392 , ASN A:394BINDING SITE FOR RESIDUE NAG A 1
02AC2SOFTWARENAG A:1 , BMA A:3 , TYR A:339 , LEU A:359 , THR A:398BINDING SITE FOR RESIDUE NAG A 2
03AC4SOFTWARENAG A:2 , MAN A:4 , MAN A:5 , TYR A:339BINDING SITE FOR RESIDUE BMA A 3
04AC5SOFTWAREBMA A:3 , MAN A:6 , MAN A:7BINDING SITE FOR RESIDUE MAN A 4
05AC6SOFTWAREBMA A:3 , ARG B:308BINDING SITE FOR RESIDUE MAN A 5
06AC7SOFTWAREMAN A:4 , GLN A:494 , HOH A:1030 , ARG B:496BINDING SITE FOR RESIDUE MAN A 6
07AC8SOFTWAREMAN A:4 , SER A:341 , ARG A:342 , THR A:355 , ILE A:356 , THR A:357 , GOL A:1001BINDING SITE FOR RESIDUE MAN A 7
08AC9SOFTWARENAG B:2 , ARG B:334 , VAL B:361 , ASP B:362 , GLN B:392 , ASN B:394 , THR B:396 , HOH B:634BINDING SITE FOR RESIDUE NAG B 1
09AD1SOFTWARENAG B:1 , BMA B:3 , SER B:337 , TYR B:339 , LEU B:359 , VAL B:361 , THR B:398BINDING SITE FOR RESIDUE NAG B 2
10AD2SOFTWARENAG B:2 , MAN B:4 , MAN B:5BINDING SITE FOR RESIDUE BMA B 3
11BC2SOFTWAREBMA B:3 , MAN B:6 , BMA B:7 , SER B:341 , HOH B:643BINDING SITE FOR RESIDUE MAN B 4
12BC3SOFTWAREBMA B:3BINDING SITE FOR RESIDUE MAN B 5
13BC4SOFTWAREMAN B:4 , GLN B:494 , HOH B:658BINDING SITE FOR RESIDUE MAN B 6
14BC5SOFTWAREMAN B:4 , ARG B:342 , SER B:344 , HOH B:578 , HOH B:644 , HOH B:645BINDING SITE FOR RESIDUE BMA B 7
15BC6SOFTWAREGLY A:243 , ARG B:393BINDING SITE FOR RESIDUE SO4 A 1011
16BC7SOFTWAREARG A:419 , ALA A:442 , GLY B:244 , HIS B:246BINDING SITE FOR RESIDUE SO4 A 1012
17BC8SOFTWAREGLY A:406 , THR A:407 , ARG A:408BINDING SITE FOR RESIDUE SO4 A 1013
18BC9SOFTWARETHR A:493 , GLN A:494 , ARG A:496 , ARG B:496BINDING SITE FOR RESIDUE SO4 A 1014
19CC1SOFTWAREMAN A:7 , SER A:344 , ILE A:474 , SER A:475BINDING SITE FOR RESIDUE GOL A 1001
20CC2SOFTWARETHR A:450 , PRO A:451 , GLU A:452 , TRP A:453 , SER A:456 , LYS A:459 , ARG A:460 , TYR B:446BINDING SITE FOR RESIDUE GOL A 1002

(-) SS Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1A:241 -B:328
2A:254 -A:312
3A:328 -B:241
4A:358 -A:418
5A:464 -A:524
6B:254 -B:312
7B:358 -B:418
8B:464 -B:524

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Met A:470 -Pro A:471
2Ser A:532 -Pro A:533
3Met B:470 -Pro B:471
4Ser B:532 -Pro B:533

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 2)

Asymmetric/Biological Unit (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_003885W359LIGHE_HUMANPolymorphism  ---A/BW478L
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 4)

Asymmetric/Biological Unit (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
B:416-422
A:522-528
B:522-528

(-) Exons   (3, 6)

Asymmetric/Biological Unit (3, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003905411ENSE00001935719chr14:106068065-106067756310IGHE_HUMAN1-1041040--
1.2ENST000003905412ENSE00001508179chr14:106067548-106067228321IGHE_HUMAN104-2111082A:228-330
B:228-330		104
104
1.3ENST000003905413ENSE00001508174chr14:106067141-106066818324IGHE_HUMAN211-3191092A:330-438
B:330-438		109
109
1.4ENST000003905414ENSE00001943927chr14:106066734-106066278457IGHE_HUMAN319-4281102A:438-545
B:438-546		108
109

(-) 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:319
 aligned with IGHE_HUMAN | P01854 from UniProtKB/Swiss-Prot  Length:428

    Alignment length:319
                                   117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417         
          IGHE_HUMAN    108 DFTPPTVKILQSSCDGGGHFPPTIQLLCLVSGYTPGTINITWLEDGQVMDVDLSTASTTQEGELASTQSELTLSQKHWLSDRTYTCQVTYQGHTFEDSTKKCADSNPRGVSAYLSRPSPFDLFIRKSPTITCLVVDLAPSKGTVNLTWSRASGKPVNHSTRKEEKQRNGTLTVTSTLPVGTRDWIEGETYQCRVTHPHLPRALMRSTTKTSGPRAAPEVYAFATPEWPGSRDKRTLACLIQNFMPEDISVQWLHNEVQLPDARHSTTQPRKTKGSGFFVFSRLEVTRAEWEQKDEFICRAVHEAASPSQTVQRAVSVNP  426
               SCOP domains d1o0va1 A:228-330 Immunoglobulin heavy chain epsilon constant domain 2, CH2-epsilon                     d1o0va2 A:331-438 Immunoglobulin heavy chain epsilon constant domain 3, CH3-epsilon                         d1o0va3 A:439-545 Immunoglobulin heavy chain epsilon constant domain 4, CH4-epsilon                         SCOP domains
               CATH domains 1o0vA01 A:228-328 Immunoglobulins                                                                     1o0vA02 A:329-435 Immunoglobulins                                                                          1o0vA03 A:436-545 Immunoglobulins                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeee..........ee.eeeeeeee....eeeeeee..ee.hhh.eeeeeeee..eeeeeeee.eehhhhhh...eeeeeee..eeeeeee......hhhhheeee...hhhhhhh....eeeeeeeee.......eeeeee....................eeeeeeee.hhhhhhh..eeeeeee......eeeeeee.........eeeeee.........eeeeeeeeeee.....eeeeee..ee.hhh.eee...ee.....eeeeeeeeeehhhhhhh..eeeeee........eeeeee.... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------L------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC ---------------------------------------------------------------------------------------------------IG_MHC ----------------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: A:228-330 UniProt: 104-211 [INCOMPLETE]                                                  -----------------------------------------------------------------------------------------------------------Exon 1.4  PDB: A:438-545 UniProt: 319-428 [INCOMPLETE]                                                       Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------------------------------------------Exon 1.3  PDB: A:330-438 UniProt: 211-319                                                                    ----------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                1o0v A  228 DFTPPTVKILQSSCDGGGHFPPTIQLLCLVSGYTPGTIQITWLEDGQVMDVDLSTASTTQEGELASTQSELTLSQKHWLSDRTYTCQVTYQGHTFEDSTKKCADSNPRGVSAYLSRPSPFDLFIRKSPTITCLVVDLAPSKGTVQLTWSRASGKPVNHSTRKEEKQRNGTLTVTSTLPVGTRDWIEGETYQCRVTHPHLPRALMRSTTKTSGPRAAPEVYAFATPEWPGSRDKRTLACLIQNFMPEDISVQWLHNEVQLPDARHSTTQPRKTKGSGFFVFSRLEVTRAEWEQKDEFICRAVHEAASPSQTVQRAVSVNP  545
                                   237       247      |256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536         
                                                   253A                                                                                                                                                                                                                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:320
 aligned with IGHE_HUMAN | P01854 from UniProtKB/Swiss-Prot  Length:428

    Alignment length:320
                                   117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427
          IGHE_HUMAN    108 DFTPPTVKILQSSCDGGGHFPPTIQLLCLVSGYTPGTINITWLEDGQVMDVDLSTASTTQEGELASTQSELTLSQKHWLSDRTYTCQVTYQGHTFEDSTKKCADSNPRGVSAYLSRPSPFDLFIRKSPTITCLVVDLAPSKGTVNLTWSRASGKPVNHSTRKEEKQRNGTLTVTSTLPVGTRDWIEGETYQCRVTHPHLPRALMRSTTKTSGPRAAPEVYAFATPEWPGSRDKRTLACLIQNFMPEDISVQWLHNEVQLPDARHSTTQPRKTKGSGFFVFSRLEVTRAEWEQKDEFICRAVHEAASPSQTVQRAVSVNPG  427
               SCOP domains d1o0vb1 B:228-330 Immunoglobulin heavy chain epsilon constant domain 2, CH2-epsilon                     d1o0vb2 B:331-438 Immunoglobulin heavy chain epsilon constant domain 3, CH3-epsilon                         d1o0vb3 B:439-546 Immunoglobulin heavy chain epsilon constant domain 4, CH4-epsilon                          SCOP domains
               CATH domains 1o0vB01 B:228-328 Immunoglobulins                                                                     1o0vB02 B:329-435 Immunoglobulins                                                                          1o0vB03 B:436-545 Immunoglobulins                                                                             - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeee..........eeeeeeeee.........eeee..eeehhhhh.eee.......eeeeeeeeehhhhhh...eeeeee....eeeeee...........eeee...hhhhhhh....eeeeeeeee.......eeeeee.........eeeeee.....eeeeeeee.hhhhhhh...eeeeee.......eeeee..........eeeeee.........eeeeeeeeeee.....eeeeee..ee.hhh.eee...ee.....eeeeeeeeeehhhhhhh..eeeeee........eeeeee..... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------L-------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC ---------------------------------------------------------------------------------------------------IG_MHC ------------------ PROSITE
           Transcript 1 (1) Exon 1.2  PDB: B:228-330 UniProt: 104-211 [INCOMPLETE]                                                  -----------------------------------------------------------------------------------------------------------Exon 1.4  PDB: B:438-546 UniProt: 319-428 [INCOMPLETE]                                                        Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------------------------------------------Exon 1.3  PDB: B:330-438 UniProt: 211-319                                                                    ------------------------------------------------------------------------------------------------------------ Transcript 1 (2)
                1o0v B  228 DFTPPTVKILQSSCDGGGHFPPTIQLLCLVSGYTPGTIQITWLEDGQVMDVDLSTASTTQEGELASTQSELTLSQKHWLSDRTYTCQVTYQGHTFEDSTKKCADSNPRGVSAYLSRPSPFDLFIRKSPTITCLVVDLAPSKGTVQLTWSRASGKPVNHSTRKEEKQRNGTLTVTSTLPVGTRDWIEGETYQCRVTHPHLPRALMRSTTKTSGPRAAPEVYAFATPEWPGSRDKRTLACLIQNFMPEDISVQWLHNEVQLPDARHSTTQPRKTKGSGFFVFSRLEVTRAEWEQKDEFICRAVHEAASPSQTVQRAVSVNPG  546
                                   237       247      |256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546
                                                   253A
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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  (3, 6)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 6)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)
(-)
Architecture: Sandwich (5577)
(-)
Topology: Immunoglobulin-like (3897)
(-)
Homologous Superfamily: Immunoglobulins (2282)
(-)
Human (Homo sapiens) (912)
1a1o0vB03B:436-545
1b1o0vA03A:436-545
1c1o0vA02A:329-435
1d1o0vB02B:329-435
1e1o0vA01A:228-328
1f1o0vB01B:228-328

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1O0V)

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (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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  1o0v
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  IGHE_HUMAN | P01854
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 Related Entries

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

UniProtKB/Swiss-Prot
        IGHE_HUMAN | P01854: 1f6a 1fp5 1g84 1ige 2ige 2wqr 2y7q 3h9y 3h9z 3ha0 4ezm 4gko 4grg 4gt7 4j4p 4ki1 5anm 5hys 5lgj 5lgk

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1O0V)