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Title :  CRYSTAL STRUCTURE OF MOUSE CD3EPSILON IN COMPLEX WITH ANTIBODY 2C11 FAB
 
Authors :  D. A. Shore, X. Zhu, I. A. Wilson
Date :  07 Mar 11  (Deposition) - 25 Jan 12  (Release) - 11 Sep 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  4.10
Chains :  Asym./Biol. Unit :  E,H,L
Keywords :  Cd3Epsilon, Antibody, T-Cell Receptor, Signalling, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. A. Fernandes, D. A. Shore, M. T. Vuong, C. Yu, X. Zhu, S. Pereira-Lopes, H. Brouwer, J. A. Fennelly, C. M. Jessup, E. J. Evans I. A. Wilson, S. J. Davis
T Cell Receptors Are Structures Capable Of Initiating Signaling In The Absence Of Large Conformational Rearrangements.
J. Biol. Chem. V. 287 13324 2012
PubMed-ID: 22262845  |  Reference-DOI: 10.1074/JBC.M111.332783

(-) Compounds

Molecule 1 - MOUSE ANTI-MOUSE CD3EPSILON ANTIBODY 2C11 LIGHT CHAIN
    CellHYBRIDOMA
    ChainsL
    EngineeredYES
    FragmentUNP RESIDUES 22-100
    Organism ScientificCRICETULUS MIGRATORIUS
    Organism Taxid10032
 
Molecule 2 - MOUSE ANTI-MOUSE CD3EPSILON ANTIBODY 2C11 HEAVY CHAIN
    CellHYBRIDOMA
    ChainsH
    EngineeredYES
    Organism ScientificCRICETULUS MIGRATORIUS
    Organism Taxid10032
 
Molecule 3 - T-CELL SURFACE GLYCOPROTEIN CD3 EPSILON CHAIN
    ChainsE
    EngineeredYES
    Expression SystemCRICETULUS GRISEUS
    Expression System CellOVARY CELLS
    Expression System Taxid10029
    GeneCD3E
    Organism CommonMOUSE
    Organism ScientificCRICETULUS MIGRATORIUS
    Organism Taxid10032
    SynonymT-CELL SURFACE ANTIGEN T3/LEU-4 EPSILON CHAIN

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit EHL

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3R08)

(-) Sites  (0, 0)

(no "Site" information available for 3R08)

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1E:21 -E:62
2H:22 -H:92
3H:142 -H:208
4L:23 -L:88
5L:134 -L:194

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Ser L:7 -Pro L:8
2Tyr L:94 -Pro L:95
3Tyr L:140 -Pro L:141
4Phe H:148 -Pro H:149
5Glu H:150 -Pro H:151
6Trp H:200 -Pro H:202

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3R08)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3R08)

(-) Exons   (0, 0)

(no "Exon" information available for 3R08)

(-) 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 E from PDB  Type:PROTEIN  Length:82
 aligned with CD3E_MOUSE | P22646 from UniProtKB/Swiss-Prot  Length:189

    Alignment length:82
                                    31        41        51        61        71        81        91       101  
           CD3E_MOUSE    22 DDAENIEYKVSISGTSVELTCPLDSDENLKWEKNGQELPQKHDKHLVLQDFSEVEDSGYYVCYTPASNKNTYLYLKARVCEY 103
               SCOP domains ---------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeee..eeeee.........eeee..ee......................eeee................... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------- Transcript
                 3r08 E   1 DDAENIEYKVSISGTSVELTCPLDSDENLKWEKNGQELPQKHDKHLVLQDFSEVEDSGYYVCYTPASNKNTYLYLKARVSEY  82
                                    10        20        30        40        50        60        70        80  

Chain H from PDB  Type:PROTEIN  Length:216
                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........eee....eeeeeee....hhhhh.eeeeeee...eeeeeeee......eee.......eeeeee....eeeeeee.......eeeeeeee....eee...eeeee........eeeee.............eeeeeeeeee.....eeee.hhh....eee.........eeeeeeeee...........eeee............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3r08 H   1 EVQLVESGGGLVQPGKSLKLSCEASGFTFSGYGMHWVRQAPGRGLESVAYITSSSINIKYADAVKGRFTVSRDNAKNLLFLQMNILKSEDTAMYYCARFDWDKNYWGQGTMVTVSSAKTTAPSVYPLAPACDSTTSTTNTVTLGCLVKGYFPEPVTVIWNSGALTSGVHTFPSVLHSGLYSLSSSVTVPSSTWPSQTVTCNVAHPASSTTVDLKIE 226
                                    10        20        30        40        50  |     59        69        79   |||  86        96  ||   107       117       127       137       147      |162      |173      |185       195||||   208       218    ||
                                                                              52A                            82A||               99|                                                  154|||    169|      180|          196|||                  223|
                                                                                                              82B|               101                                                   156||     171       183           199||                   226
                                                                                                               82C                                                                      157|                              200|                      
                                                                                                                                                                                         162                               202                      

Chain L from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eee.....eeeeee........eeeeee......eeee.............eeee....eeeeee...hhhhh.eeeeee...........eeeee.......eeeee..hhhhhhhh...eeeeee.........eeee..ee.......ee..........eeeeee..hhhhhh...eeeeee........eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3r08 L   1 DIQMTQSPSSLPASLGDRVTINCQASQDISNYLNWYQQKPGKAPKLLIYYTNKLADGVPSRFSGSGSGRDSSFTISSLESEDIGSYYCQQYYNYPWTFGPGTKLEIKRADAKPTVSIFPPSSEQLGTGSATLVCFVNNFYPKDINVKWKVDGSEKRDGVLQSVTDQDSKDSTYSLSSTLSLTKADYERHNLYTCEVTHKTSTAAIVKTLNRNE 213
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210   

   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  (0, 0)

(no "SCOP Domain" information available for 3R08)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3R08)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3R08)

(-) Gene Ontology  (34, 34)

Asymmetric/Biological Unit(hide GO term definitions)
Chain E   (CD3E_MOUSE | P22646)
molecular function
    GO:0017124    SH3 domain binding    Interacting selectively and non-covalently with a SH3 domain (Src homology 3) of a protein, small protein modules containing approximately 50 amino acid residues found in a great variety of intracellular or membrane-associated proteins.
    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:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
    GO:0004871    signal transducer activity    Conveys a signal across a cell to trigger a change in cell function or state. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response.
    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:0031295    T cell costimulation    The process of providing, via surface-bound receptor-ligand pairs, a second, antigen-independent, signal in addition to that provided by the T cell receptor to augment T cell activation.
    GO:0033077    T cell differentiation in thymus    The process in which a precursor cell type acquires the specialized features of a T cell via a differentiation pathway dependent upon transit through the thymus.
    GO:0050852    T cell receptor signaling pathway    A series of molecular signals initiated by the cross-linking of an antigen receptor on a T cell.
    GO:0097190    apoptotic signaling pathway    A series of molecular signals which triggers the apoptotic death of a cell. The pathway starts with reception of a signal, and ends when the execution phase of apoptosis is triggered.
    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.
    GO:0046649    lymphocyte activation    A change in morphology and behavior of a lymphocyte resulting from exposure to a specific antigen, mitogen, cytokine, chemokine, cellular ligand, or soluble factor.
    GO:0010629    negative regulation of gene expression    Any process that decreases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:0045879    negative regulation of smoothened signaling pathway    Any process that stops, prevents, or reduces the frequency, rate or extent of smoothened signaling.
    GO:0045060    negative thymic T cell selection    The process of elimination of immature T cells in the thymus which react strongly with self-antigens.
    GO:0050870    positive regulation of T cell activation    Any process that activates or increases the frequency, rate or extent of T cell activation.
    GO:0002669    positive regulation of T cell anergy    Any process that activates or increases the frequency, rate, or extent of T cell anergy.
    GO:0042102    positive regulation of T cell proliferation    Any process that activates or increases the rate or extent of T cell proliferation.
    GO:0046641    positive regulation of alpha-beta T cell proliferation    Any process that activates or increases the frequency, rate or extent of alpha-beta T cell proliferation.
    GO:0050850    positive regulation of calcium-mediated signaling    Any process that activates or increases the frequency, rate or extent of calcium-mediated signaling.
    GO:0010628    positive regulation of gene expression    Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:0032729    positive regulation of interferon-gamma production    Any process that activates or increases the frequency, rate, or extent of interferon-gamma production. Interferon-gamma is also known as type II interferon.
    GO:0045086    positive regulation of interleukin-2 biosynthetic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of interleukin-2.
    GO:0032753    positive regulation of interleukin-4 production    Any process that activates or increases the frequency, rate, or extent of interleukin-4 production.
    GO:0050731    positive regulation of peptidyl-tyrosine phosphorylation    Any process that activates or increases the frequency, rate or extent of the phosphorylation of peptidyl-tyrosine.
    GO:0007584    response to nutrient    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nutrient stimulus.
cellular component
    GO:0042101    T cell receptor complex    A protein complex that contains a disulfide-linked heterodimer of T cell receptor (TCR) chains, which are members of the immunoglobulin superfamily, and mediates antigen recognition, ultimately resulting in T cell activation. The TCR heterodimer is associated with the CD3 complex, which consists of the nonpolymorphic polypeptides gamma, delta, epsilon, zeta, and, in some cases, eta (an RNA splice variant of zeta) or Fc epsilon chains.
    GO:0042105    alpha-beta T cell receptor complex    A T cell receptor complex in which the TCR heterodimer comprises alpha and beta chains, associated with the CD3 complex; recognizes a complex consisting of an antigen-derived peptide bound to a class I or class II MHC protein.
    GO:0005911    cell-cell junction    A cell junction that forms a connection between two or more cells in a multicellular organism; excludes direct cytoplasmic junctions such as ring canals.
    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:0001772    immunological synapse    An area of close contact between a lymphocyte (T-, B-, or natural killer cell) and a target cell formed through the clustering of particular signaling and adhesion molecules and their associated membrane rafts on both the lymphocyte and the target cell and facilitating activation of the lymphocyte, transfer of membrane from the target cell to the lymphocyte, and in some situations killing of the target cell through release of secretory granules and/or death-pathway ligand-receptor interaction.
    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: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 H:150 - Pro H:151   [ RasMol ]  
    Phe H:148 - Pro H:149   [ RasMol ]  
    Ser L:7 - Pro L:8   [ RasMol ]  
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 Related Entries

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

UniProtKB/Swiss-Prot
        CD3E_MOUSE | P226461jbj 1xmw 2k4f

(-) Related Entries Specified in the PDB File

3r06 THE APO STRUCTURE OF ANTIBODY 2C11 FAB