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(-) Description

Title :  THE HIGH RESOLUTION CRYSTAL STRUCTURE OF IGE FC
 
Authors :  B. Dhaliwal, B. J. Sutton, A. J. Beavil
Date :  26 Aug 09  (Deposition) - 03 Nov 10  (Release) - 12 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Immune System, Immunoglobulin Domain, Glycoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. D. Holdom, A. M. Davies, J. E. Nettleship, S. C. Bagby, B. Dhaliwal, E. Girardi, J. Hunt, H. J. Gould, A. J. Beavil, J. M. Mcdonnell, R. J. Owens, B. J. Sutton
Conformational Changes In Ige Contribute To Its Uniquely Slow Dissociation Rate From Receptor Fceri
Nat. Struct. Mol. Biol. V. 18 571 2011
PubMed-ID: 21516097  |  Reference-DOI: 10.1038/NSMB.2044
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - IG EPSILON CHAIN C REGION
    Chains: A, B
    Engineered: YES
    Expression System: MUS MUSCULUS
    Expression System Cell Line: MOUSE MYELOMA NS0
    Expression System Plasmid: PEE6
    Expression System Taxid: 10090
    Fragment: FC FRAGMENT, RESIDUES 105-427
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: IMMUNOGLOBULIN E, IGE FC

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 18)

Asymmetric/Biological Unit (7, 18)
No.NameCountTypeFull Name
1BMA2Ligand/IonBETA-D-MANNOSE
2GOL2Ligand/IonGLYCEROL
3MAN4Ligand/IonALPHA-D-MANNOSE
4NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
5PG41Ligand/IonTETRAETHYLENE GLYCOL
6SO44Ligand/IonSULFATE ION
7TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:362 , GLN A:392 , ASN A:394 , THR A:396 , NAG A:602BINDING SITE FOR RESIDUE NAG A 946
02AC2SOFTWARETYR A:339 , LEU A:359 , NAG A:601 , BMA A:603BINDING SITE FOR RESIDUE NAG A 947
03AC3SOFTWARETYR A:339 , NAG A:602 , MAN A:604 , MAN A:605 , HOH A:888BINDING SITE FOR RESIDUE BMA A 948
04AC4SOFTWAREBMA A:603 , HOH A:818BINDING SITE FOR RESIDUE MAN A 949
05AC5SOFTWAREGLN A:494 , BMA A:603 , HOH A:858BINDING SITE FOR RESIDUE MAN A 950
06AC6SOFTWARETHR A:493 , GLN A:494 , ARG A:496 , HOH A:754 , HOH A:786 , ARG B:496BINDING SITE FOR RESIDUE SO4 A 951
07AC7SOFTWARETHR A:407 , ARG A:408BINDING SITE FOR RESIDUE SO4 A 952
08AC8SOFTWAREARG A:496 , LYS A:497 , ARG B:308BINDING SITE FOR RESIDUE SO4 A 953
09AC9SOFTWAREARG A:419 , ALA A:442 , GLY B:244 , HIS B:246BINDING SITE FOR RESIDUE GOL A 954
10BC1SOFTWAREASP A:242 , GLY A:243 , SER B:324 , ARG B:393BINDING SITE FOR RESIDUE GOL A 955
11BC2SOFTWARESER A:344 , ILE A:474 , SER A:475 , VAL A:476 , HOH A:817 , HOH A:749BINDING SITE FOR RESIDUE TRS A 956
12BC3SOFTWARELYS A:235 , LEU A:253A , LEU A:255 , GLN A:294 , GLU A:296 , HOH A:746 , HOH B:719 , HOH B:701 , LYS B:235 , LEU B:253A , LEU B:255 , GLN B:294 , GLU B:296 , HOH B:919BINDING SITE FOR RESIDUE PG4 A 957
13BC4SOFTWAREGLY B:406 , THR B:407 , ARG B:408 , HOH B:775BINDING SITE FOR RESIDUE SO4 B 946
14BC5SOFTWAREASP B:362 , GLN B:392 , ASN B:394 , THR B:396 , NAG B:605 , HOH B:843BINDING SITE FOR RESIDUE NAG B 947
15BC6SOFTWARETYR B:339 , LEU B:359 , VAL B:361 , THR B:398 , NAG B:604 , BMA B:606 , HOH B:853BINDING SITE FOR RESIDUE NAG B 948
16BC7SOFTWARETYR B:339 , NAG B:605 , MAN B:607 , MAN B:608BINDING SITE FOR RESIDUE BMA B 949
17BC8SOFTWARESER B:341 , BMA B:606BINDING SITE FOR RESIDUE MAN B 950
18BC9SOFTWAREBMA B:606BINDING SITE FOR RESIDUE MAN B 951

(-) 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:225-330		104
107
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 d2wqra1 A:228-330 automated matches                                                                     d2wqra2 A:331-438 automated matches                                                                         d2wqra3 A:439-545 automated matches                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee..........eeeeeeee.......eeeeeee.....hhh.eeeeeee....eeeeeeeeeehhhhhh...eeeeeee...eeeeee...........eeee...hhhhhhh....eeeeeeeee.......eeeeee...........eeee.....eeeeeeee..hhhhhh...eeeeee.......eeeee..........eeeeee.........eeeeeeeee.......eeeeee..ee.hhh.eee...........eeeeeeeeehhhhhhh..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)
                2wqr 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:323
 aligned with IGHE_HUMAN | P01854 from UniProtKB/Swiss-Prot  Length:428

    Alignment length:323
                                   114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424   
          IGHE_HUMAN    105 CSRDFTPPTVKILQSSCDGGGHFPPTIQLLCLVSGYTPGTINITWLEDGQVMDVDLSTASTTQEGELASTQSELTLSQKHWLSDRTYTCQVTYQGHTFEDSTKKCADSNPRGVSAYLSRPSPFDLFIRKSPTITCLVVDLAPSKGTVNLTWSRASGKPVNHSTRKEEKQRNGTLTVTSTLPVGTRDWIEGETYQCRVTHPHLPRALMRSTTKTSGPRAAPEVYAFATPEWPGSRDKRTLACLIQNFMPEDISVQWLHNEVQLPDARHSTTQPRKTKGSGFFVFSRLEVTRAEWEQKDEFICRAVHEAASPSQTVQRAVSVNPG  427
               SCOP domains d2wqrb1 B:225-330 automated matches                                                                        d2wqrb2 B:331-438 automated matches                                                                         d2wqrb3 B:439-546 automated matches                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------C1-set-2wqrB01 B:450-536                                                               ---------- Pfam domains (1)
           Pfam domains (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------C1-set-2wqrB02 B:450-536                                                               ---------- Pfam domains (2)
           Pfam domains (3) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------C1-set-2wqrB03 B:450-536                                                               ---------- Pfam domains (3)
           Pfam domains (4) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------C1-set-2wqrB04 B:450-536                                                               ---------- Pfam domains (4)
           Pfam domains (5) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------C1-set-2wqrB05 B:450-536                                                               ---------- Pfam domains (5)
           Pfam domains (6) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------C1-set-2wqrB06 B:450-536                                                               ---------- Pfam domains (6)
         Sec.struct. author hhhhh....eeeeee..........eeeeeeee.......eeeeeee.....hhh.eeeeeee....eeeeeeeeeehhhhhh...eeeeeee...eeeeee...........eeeee..hhhhhhh....eeeeeeeee.......eeeeee.........eeeeee.....eeeeeeee..hhhhhh...eeeeee.......eeeee..........eeeeee.........eeeeeeeee.......eeeeee..ee.hhh.eee...........eeeeeeeeehhhhhhh..eeeeee........eeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------L-------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC ---------------------------------------------------------------------------------------------------IG_MHC ------------------ PROSITE
           Transcript 1 (1) Exon 1.2  PDB: B:225-330 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)
                2wqr B  225 CSRDFTPPTVKILQSSCDGGGHFPPTIQLLCLVSGYTPGTIQITWLEDGQVMDVDLSTASTTQEGELASTQSELTLSQKHWLSDRTYTCQVTYQGHTFEDSTKKCADSNPRGVSAYLSRPSPFDLFIRKSPTITCLVVDLAPSKGTVQLTWSRASGKPVNHSTRKEEKQRNGTLTVTSTLPVGTRDWIEGETYQCRVTHPHLPRALMRSTTKTSGPRAAPEVYAFATPEWPGSRDKRTLACLIQNFMPEDISVQWLHNEVQLPDARHSTTQPRKTKGSGFFVFSRLEVTRAEWEQKDEFICRAVHEAASPSQTVQRAVSVNPG  546
                                   234       244      253A       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543   
                                                      253A
   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  (1, 6)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2WQR)

(-) Pfam Domains  (1, 6)

Asymmetric/Biological Unit
(-)
Clan: Ig (577)
(-)
Family: C1-set (338)
(-)
Homo sapiens (Human) (218)
1aC1-set-2wqrB01B:450-536
1bC1-set-2wqrB02B:450-536
1cC1-set-2wqrB03B:450-536
1dC1-set-2wqrB04B:450-536
1eC1-set-2wqrB05B:450-536
1fC1-set-2wqrB06B:450-536

(-) 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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  2wqr
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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 1o0v 2ige 2y7q 3h9y 3h9z 3ha0 4ezm 4gko 4grg 4gt7 4j4p 4ki1 5anm 5hys 5lgj 5lgk

(-) Related Entries Specified in the PDB File

1f6a STRUCTURE OF THE HUMAN IGE-FC BOUND TO ITS HIGH AFFINITYRECEPTOR FC(EPSILON)RI( ALPHA)
1fp5 CRYSTAL STRUCTURE ANALYSIS OF THE HUMAN IGE -FC CEPSILON3-CEPSILON4 FRAGMENT.
1g84 THE SOLUTION STRUCTURE OF THE C EPSILON2 DOMAIN FROM IGE
1ige FC FRAGMENT (IGE'CL) (THEORETICAL MODEL)
1o0v THE CRYSTAL STRUCTURE OF IGE FC REVEALS AN ASYMMETRICALLYBENT CONFORMATION