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(-) Description

Title :  CD23 LECTIN DOMAIN, CALCIUM 2+-BOUND
 
Authors :  B. A. Wurzburg
Date :  19 May 06  (Deposition) - 20 Jun 06  (Release) - 05 Oct 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
Chains :  Asym./Biol. Unit :  B
Keywords :  C-Type Lectin, Calcium-Bound, Lectin Domain, Low Affinity Ige Receptor, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  B. A. Wurzburg, S. S. Tarchevskaya, T. S. Jardetzky
Structural Changes In The Lectin Domain Of Cd23, The Low-Affinity Ige Receptor, Upon Calcium Binding.
Structure V. 14 1049 2006
PubMed-ID: 16765898  |  Reference-DOI: 10.1016/J.STR.2006.03.017

(-) Compounds

Molecule 1 - LOW AFFINITY IMMUNOGLOBULIN EPSILON FC RECEPTOR (LYMPHOCYTE IGE RECEPTOR) (FC-EPSILON-RII) (IMMUNOGLOBULIN E-BINDING FACTOR) (CD23 ANTIGEN)
    ChainsB
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System CommonFALL ARMYWORM
    Expression System PlasmidPBACGUS-3
    Expression System StrainSF+
    Expression System Taxid7108
    Expression System Vector TypeRECOMBINANT BACULOVIRUS
    FragmentLECTIN DOMAIN
    GeneFCER2
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU B:249 , THR B:251 , ASN B:269 , ASP B:270 , HOH B:323 , HOH B:324BINDING SITE FOR RESIDUE CA B 322

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1B:160 -B:288
2B:163 -B:174
3B:191 -B:282
4B:259 -B:273

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Glu B:249 -Pro B:250

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_035388R284QFCER2_HUMANPolymorphism8102872BR284Q

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

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1C_TYPE_LECTIN_2PS50041 C-type lectin domain profile.FCER2_HUMAN170-277  1B:170-277
2C_TYPE_LECTIN_1PS00615 C-type lectin domain signature.FCER2_HUMAN259-282  1B:259-282

(-) Exons   (3, 3)

Asymmetric/Biological Unit (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003466641aENSE00001237098chr19:7766997-776690593FCER2_HUMAN-00--
1.2ENST000003466642ENSE00001397092chr19:7764731-7764625107FCER2_HUMAN1-880--
1.4ENST000003466644ENSE00000874617chr19:7763740-7763627114FCER2_HUMAN8-46390--
1.5ENST000003466645ENSE00000671471chr19:7763295-776324254FCER2_HUMAN46-64190--
1.6ENST000003466646ENSE00000671470chr19:7762475-776241363FCER2_HUMAN64-85220--
1.7ENST000003466647ENSE00000671469chr19:7762184-776212263FCER2_HUMAN85-106220--
1.8ENST000003466648ENSE00001052912chr19:7761961-776189963FCER2_HUMAN106-127220--
1.9ENST000003466649ENSE00000671467chr19:7761800-776171190FCER2_HUMAN127-157310--
1.10ENST0000034666410ENSE00000671466chr19:7755443-7755292152FCER2_HUMAN157-207511B:160-20748
1.11ENST0000034666411ENSE00000671465chr19:7755151-7755045107FCER2_HUMAN208-243361B:208-24336
1.12bENST0000034666412bENSE00001517758chr19:7754316-7753663654FCER2_HUMAN243-321791B:243-288 (gaps)46

(-) 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 B from PDB  Type:PROTEIN  Length:124
 aligned with FCER2_HUMAN | P06734 from UniProtKB/Swiss-Prot  Length:321

    Alignment length:129
                                   169       179       189       199       209       219       229       239       249       259       269       279         
          FCER2_HUMAN   160 CNTCPEKWINFQRKCYYFGKGTKQWVHARYACDDMEGQLVSIHSPEEQDFLTKHASHTGSWIGLRNLDLKGEFIWVDGSHVDYSNWAPGEPTSRSQGEDCVMMRGSGRWNDAFCDRKLGAWVCDRLATC 288
               SCOP domains d2h2tb_ B: automated matches                                                                                                      SCOP domains
               CATH domains ------2h2tB01 B:166-286 Mannose-Binding Protein A, subunit A                                                                   -- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eee..eeeeeeeeeehhhhhhhhhhhh..ee....hhhhhhhhhh......eeeeeeeehhh.eeee..................-----.eeee.....eeee.....eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------Q---- SAPs(SNPs)
                PROSITE (1) ----------C_TYPE_LECTIN_2  PDB: B:170-277 UniProt: 170-277                                                            ----------- PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------------C_TYPE_LECTIN_1         ------ PROSITE (2)
           Transcript 1 (1) Exon 1.10  PDB: B:160-207 UniProt: 157-207      Exon 1.11  PDB: B:208-243           --------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------------------Exon 1.12b  PDB: B:243-288 (gaps) [INCOMPLETE] Transcript 1 (2)
                 2h2t B 160 CNTCPEKWINFQRKCYYFGKGTKQWVHARYACDDMEGQLVSIHSPEEQDFLTKRASHTGSWIGLRNLDLKGEFIWVDGSHVDYSNWAPGEPTS-----DCVMMRGSGRWNDAFCDRKLGAWVCDRLATC 288
                                   169       179       189       199       209       219       229       239       249  |    259       269       279         
                                                                                                                      252   258                              

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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2H2T)

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)
Chain B   (FCER2_HUMAN | P06734)
molecular function
    GO:0019863    IgE binding    Interacting selectively and non-covalently with an immunoglobulin of the IgE isotype.
    GO:0030246    carbohydrate binding    Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
    GO:0005178    integrin binding    Interacting selectively and non-covalently with an integrin.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0007219    Notch signaling pathway    A series of molecular signals initiated by the binding of an extracellular ligand to the receptor Notch on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0002925    positive regulation of humoral immune response mediated by circulating immunoglobulin    Any process that activates or increases the frequency, rate, or extent of a humoral immune response mediated by circulating immunoglobulin.
    GO:0051712    positive regulation of killing of cells of other organism    Any process that activates or increases the frequency, rate or extent of the killing by an organism of cells in another organism.
    GO:0051000    positive regulation of nitric-oxide synthase activity    Any process that activates or increases the activity of the enzyme nitric-oxide synthase.
    GO:0051770    positive regulation of nitric-oxide synthase biosynthetic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of a nitric oxide synthase enzyme.
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:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    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: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: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
        FCER2_HUMAN | P067341hli 1kje 1t8c 1t8d 2h2r 4ezm 4g96 4g9a 4gi0 4gj0 4gjx 4gk1 4gko 4j6j 4j6k 4j6l 4j6m 4j6n 4j6p 4j6q 4ki1 5lgk

(-) Related Entries Specified in the PDB File

1hlj MODEL OF THE HUMAN CD23 LECTIN DOMAIN
1kje MODEL OF THE HUMAN CD23 LECTIN DOMAIN
1t8c NMR STRUCTURE OF THE HUMAN CD23 LECTIN DOMAIN (DER P I FRAGMENT)
1t8d NMR STRUCTURE OF THE HUMAN CD23 LECTIN DOMAIN (DER P I FRAGMENT)
2h2r CRYSTAL STRUCTURE OF THE HUMAN CD23 LECTIN DOMAIN, APO FORM