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(-) Description

Title :  CRYSTAL STRUCTURE OF MURINE IG-BETA (CD79B) HOMODIMER
 
Authors :  S. Radaev, P. D. Sun
Date :  30 Oct 09  (Deposition) - 25 Aug 10  (Release) - 25 Aug 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.11
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Cd79B, Cd79A, Ig-Beta, Bcr, Ig Domain, V-Set, Immunoglobulin Domain, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Radaev, Z. Zou, P. Tolar, K. Nguyen, A. Nguyen, P. D. Krueger, N. Stutzman, S. Pierce, P. D. Sun
Structural And Functional Studies Of Igalphabeta And Its Assembly With The B Cell Antigen Receptor.
Structure V. 18 934 2010
PubMed-ID: 20696394  |  Reference-DOI: 10.1016/J.STR.2010.04.019

(-) Compounds

Molecule 1 - B-CELL ANTIGEN RECEPTOR COMPLEX-ASSOCIATED PROTEIN BETA CHAIN
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneCD79B, IGB
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymIG-BETA, B-CELL-SPECIFIC GLYCOPROTEIN B29, IMMUNOGLOBULIN- ASSOCIATED B29 PROTEIN

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS B:49 , PRO B:50 , ARG B:51 , PHE B:52BINDING SITE FOR RESIDUE SO4 B 900
2AC2SOFTWAREARG A:57 , TYR A:112 , GLY A:143 , PHE A:144BINDING SITE FOR RESIDUE SO4 A 800

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:65 -A:120
2B:43 -B:124
3B:65 -B:120
4B:135 -A:135

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1His B:49 -Pro B:50
2His A:49 -Pro A:50

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3KHO)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3KHO)

(-) Exons   (0, 0)

(no "Exon" information available for 3KHO)

(-) 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:88
 aligned with CD79B_MOUSE | P15530 from UniProtKB/Swiss-Prot  Length:228

    Alignment length:99
                                    55        65        75        85        95       105       115       125       135         
          CD79B_MOUSE    46 IWQHPRFAAKKRSSMVKFHCYTNHSGALTWFRKRGSQQPQELVSEEGRIVQTQNGSVYTLTIQNIQYEDNGIYFCKQKCDSANHNVTDSCGTELLVLGF 144
               SCOP domains d3khoa_ A: automated matches                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee..eeee.....eeeeee......eeeeee......ee...--..eeeeee..eeeeee...hhhhheeeeeee.---------....eeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                 3kho A  46 IWQHPRFAAKKRSSMVKFHCYTNHSGALTWFRKRGSQQPQELVS--GRIVQTQNGSVYTLTIQNIQYEDNGIYFCKQK---------DSCGTELLVLGF 144
                                    55        65        75        85   |  | 95       105       115       | -       135         
                                                                      89 92                            123       133           

Chain B from PDB  Type:PROTEIN  Length:95
 aligned with CD79B_MOUSE | P15530 from UniProtKB/Swiss-Prot  Length:228

    Alignment length:100
                                    52        62        72        82        92       102       112       122       132       142
          CD79B_MOUSE    43 CSQIWQHPRFAAKKRSSMVKFHCYTNHSGALTWFRKRGSQQPQELVSEEGRIVQTQNGSVYTLTIQNIQYEDNGIYFCKQKCDSANHNVTDSCGTELLVL 142
               SCOP domains d3khob_ B: automated matches                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) V-set-3khoB01 B:43-141                                                                             - Pfam domains (1)
           Pfam domains (2) V-set-3khoB02 B:43-141                                                                             - Pfam domains (2)
         Sec.struct. author ....eee..eeee.....eeeeee......eeeeee.....eee..hhhh.eeeeee..eeeeee...hhhhheeeeeee..-----..ee...eeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------- Transcript
                 3kho B  43 CSQIWQHPRFAAKKRSSMVKFHCYTNHSGALTWFRKRGSQQPQELVSEEGRIVQTQNGSVYTLTIQNIQYEDNGIYFCKQKC-----NVTDSCGTELLVL 142
                                    52        62        72        82        92       102       112       122 |     132       142
                                                                                                           124   130            

   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  (0, 0)

(no "CATH Domain" information available for 3KHO)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: Ig (577)
(-)
Family: V-set (144)

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (CD79B_MOUSE | P15530)
molecular function
    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).
    GO:0004888    transmembrane signaling receptor activity    Combining with an extracellular or intracellular signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity or state as part of signal transduction.
biological process
    GO:0030183    B cell differentiation    The process in which a precursor cell type acquires the specialized features of a B cell. A B cell is a lymphocyte of B lineage with the phenotype CD19-positive and capable of B cell mediated immunity.
    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:0002250    adaptive immune response    An immune response mediated by cells expressing specific receptors for antigen produced through a somatic diversification process, and allowing for an enhanced secondary response to subsequent exposures to the same antigen (immunological memory).
    GO:0007166    cell surface receptor signaling pathway    A series of molecular signals initiated by activation of a receptor on the surface of a cell. The pathway begins with binding of an extracellular ligand to a cell surface receptor, or for receptors that signal in the absence of a ligand, by ligand-withdrawal or the activity of a constitutively active receptor. The pathway ends with regulation of a downstream cellular process, e.g. transcription.
    GO:0002376    immune system process    Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
cellular component
    GO:0019815    B cell receptor complex    An immunoglobulin complex that is present in the plasma membrane of B cells and that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains and a signaling subunit, a heterodimer of the Ig-alpha and Ig-beta proteins.
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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: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:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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
        CD79B_MOUSE | P155303khq

(-) Related Entries Specified in the PDB File

3kg5 3khq