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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HUMAN CD23 LECTIN DOMAIN, APO FORM
 
Authors :  B. A. Wurzburg
Date :  19 May 06  (Deposition) - 20 Jun 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  C-Type Lectin, Apo Form, 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
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LOW AFFINITY IMMUNOGLOBULIN EPSILON FC RECEPTOR (LYMPHOCYTE IGE RECEPTOR) (FC-EPSILON-RII)(IMMUNOGLOBULIN E-BINDING FACTOR) (CD23 ANTIGEN)
    ChainsA, B
    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

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2H2R)

(-) Sites  (0, 0)

(no "Site" information available for 2H2R)

(-) SS Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1A:160 -A:288
2A:163 -A:174
3A:191 -A:282
4A:259 -A:273
5B:160 -B:288
6B:163 -B:174
7B:191 -B:282
8B:259 -B:273

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Glu A:249 -Pro A:250
2Glu B:249 -Pro B:250

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 2)

Asymmetric/Biological Unit (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_035388R284QFCER2_HUMANPolymorphism8102872A/BR284Q

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

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1C_TYPE_LECTIN_2PS50041 C-type lectin domain profile.FCER2_HUMAN170-277
 
  2A:170-277
B:170-277
2C_TYPE_LECTIN_1PS00615 C-type lectin domain signature.FCER2_HUMAN259-282
 
  2A:259-282
B:259-282

(-) Exons   (3, 6)

Asymmetric/Biological Unit (3, 6)
 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_HUMAN157-207512A:158-207
B:158-207
50
50
1.11ENST0000034666411ENSE00000671465chr19:7755151-7755045107FCER2_HUMAN208-243362A:208-243
B:208-243
36
36
1.12bENST0000034666412bENSE00001517758chr19:7754316-7753663654FCER2_HUMAN243-321792A:243-292
B:243-291
50
49

(-) 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:135
 aligned with FCER2_HUMAN | P06734 from UniProtKB/Swiss-Prot  Length:321

    Alignment length:135
                                   167       177       187       197       207       217       227       237       247       257       267       277       287     
          FCER2_HUMAN   158 FVCNTCPEKWINFQRKCYYFGKGTKQWVHARYACDDMEGQLVSIHSPEEQDFLTKHASHTGSWIGLRNLDLKGEFIWVDGSHVDYSNWAPGEPTSRSQGEDCVMMRGSGRWNDAFCDRKLGAWVCDRLATCTPPA 292
               SCOP domains d2h2ra_ A: automated matches                                                                                                            SCOP domains
               CATH domains --------2h2rA01 A:166-286 Mannose-Binding Protein A, subunit A                                                                   ------ CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.....eee..eeeeeeeeeehhhhhhhhhhhh..ee....hhhhhhhhhh......eeeeeeee.....eee......................eeeeee.....eeee.....eeeeeeeee.eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------Q-------- SAPs(SNPs)
                PROSITE (1) ------------C_TYPE_LECTIN_2  PDB: A:170-277 UniProt: 170-277                                                            --------------- PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------------------C_TYPE_LECTIN_1         ---------- PROSITE (2)
           Transcript 1 (1) Exon 1.10  PDB: A:158-207 UniProt: 157-207        Exon 1.11  PDB: A:208-243           ------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------------------------Exon 1.12b  PDB: A:243-292 UniProt: 243-321        Transcript 1 (2)
                 2h2r A 158 FVCNTCPEKWINFQRKCYYFGKGTKQWVHARYACDDMEGQLVSIHSPEEQDFLTKRASHTGSWIGLRNLDLKGEFIWVDGSHVDYSNWAPGEPTSRSQSEDCVMMRGSGRWNDAFCDRKLGAWVCDRLATCTPPA 292
                                   167       177       187       197       207       217       227       237       247       257       267       277       287     

Chain B from PDB  Type:PROTEIN  Length:134
 aligned with FCER2_HUMAN | P06734 from UniProtKB/Swiss-Prot  Length:321

    Alignment length:134
                                   167       177       187       197       207       217       227       237       247       257       267       277       287    
          FCER2_HUMAN   158 FVCNTCPEKWINFQRKCYYFGKGTKQWVHARYACDDMEGQLVSIHSPEEQDFLTKHASHTGSWIGLRNLDLKGEFIWVDGSHVDYSNWAPGEPTSRSQGEDCVMMRGSGRWNDAFCDRKLGAWVCDRLATCTPP 291
               SCOP domains d2h2rb_ B: automated matches                                                                                                           SCOP domains
               CATH domains --------2h2rB01 B:166-286 Mannose-Binding Protein A, subunit A                                                                   ----- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.....eee..eeeeeeeeeehhhhhhhhhhhh..ee....hhhhhhhhhhhh....eeeeeeee.....eee......................eeeeee.....eeeee....eeeeeeeee.eee.. 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:158-207 UniProt: 157-207        Exon 1.11  PDB: B:208-243           ------------------------------------------------ Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------------------------Exon 1.12b  PDB: B:243-291 UniProt: 243-321       Transcript 1 (2)
                 2h2r B 158 FVCNTCPEKWINFQRKCYYFGKGTKQWVHARYACDDMEGQLVSIHSPEEQDFLTKRASHTGSWIGLRNLDLKGEFIWVDGSHVDYSNWAPGEPTSRSQSEDCVMMRGSGRWNDAFCDRKLGAWVCDRLATCTPP 291
                                   167       177       187       197       207       217       227       237       247       257       267       277       287    

   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, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2H2R)

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,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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  Cis Peptide Bonds
    Glu A:249 - Pro A:250   [ RasMol ]  
    Glu B:249 - Pro B:250   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        FCER2_HUMAN | P067341hli 1kje 1t8c 1t8d 2h2t 4ezm 4g96 4g9a 4gi0 4gj0 4gjx 4gk1 4gko 4j6j 4j6k 4j6l 4j6m 4j6n 4j6p 4j6q 4ki1 5lgk

(-) Related Entries Specified in the PDB File

1hli MODEL OF THE HUMAN CD23 LECTIN DOMAIN
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
2h2t CRYSTAL STRUCTURE OF THE HUMAN CD23 LECTIN DOMAIN WITH BOUND CALCIUM ION