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Title :  A 3-DIMENSIONAL MODEL FOR THE CD40 LIGAND REVEALS A CLOSE SIMILARITY TO THE TUMOR NECROSIS FACTORS
 
Authors :  M. C. Peitsch, C. V. Jongeneel
Date :  10 Jul 92  (Deposition) - 31 Oct 93  (Release) - 01 Apr 03  (Revision)
Method :  THEORETICAL MODEL
Resolution :  NOT APPLICABLE
Chains :  Theor. Model :  A,B,C
Keywords :  Cytokine (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. C. Peitsch, C. V. Jongeneel
A 3-D Model For The Cd40 Ligand Predicts That It Is A Compact Trimer Similar To The Tumor Necrosis Factors.
Int. Immunol. V. 5 233 1993
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CD40
    ChainsA, B, C
    EngineeredYES

 Structural Features

(-) Chains, Units

  
Theoretical Model 

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1CDA)

(-) Sites  (0, 0)

(no "Site" information available for 1CDA)

(-) SS Bonds  (3, 3)

Theoretical Model
No.Residues
1A:63 -A:103
2B:63 -B:103
3C:63 -C:103

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1CDA)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1CDA)

(-) PROSITE Motifs  (2, 6)

Theoretical Model (2, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TNF_2PS50049 TNF family profile.CD40L_MOUSE122-260
 
 
  3A:8-146
B:8-146
C:8-146
2TNF_1PS00251 TNF family signature.CD40L_MOUSE160-176
 
 
  3A:46-62
B:46-62
C:46-62

(-) Exons   (0, 0)

(no "Exon" information available for 1CDA)

(-) Sequences/Alignments

Theoretical Model
   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:146
 aligned with CD40L_MOUSE | P27548 from UniProtKB/Swiss-Prot  Length:260

    Alignment length:146
                                   124       134       144       154       164       174       184       194       204       214       224       234       244       254      
          CD40L_MOUSE   115 GDEDPQIAAHVVSEANSNAASVLQWAKKGYYTMKSNLVMLENGKQLTVKREGLYYVYTQVTFCSNREPSSQRPFIVGLWLKPSSGSERILLKAANTHSSSQLCEQQSVHLGGVFELQAGASVFVNVTEASQVIHRVGFSSFGLLKL 260
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeee...................eee...eee...eeee...eeeeeeeeeeeeee........eeeeeeeee..eeeeeeeeeee........eeeeeeeeeeeee..eeeeeeee............eeeeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------TNF_2  PDB: A:8-146 UniProt: 122-260                                                                                                        PROSITE (1)
                PROSITE (2) ---------------------------------------------TNF_1            ------------------------------------------------------------------------------------ PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1cda A   1 GDEDPQIAAHVVSEANSNAASVLQWAKKGYYTMKSNLVMLENGKQLTVKREGLYYVYTQVTFCSNREPSSQRPFIVGLWLKPSIGSERILLKAANTHSSSQLCEQQSVHLGGVFELQAGASVFVNVTEASQVIHRVGFSSFGLLKL 146
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140      

Chain B from PDB  Type:PROTEIN  Length:146
 aligned with CD40L_MOUSE | P27548 from UniProtKB/Swiss-Prot  Length:260

    Alignment length:146
                                   124       134       144       154       164       174       184       194       204       214       224       234       244       254      
          CD40L_MOUSE   115 GDEDPQIAAHVVSEANSNAASVLQWAKKGYYTMKSNLVMLENGKQLTVKREGLYYVYTQVTFCSNREPSSQRPFIVGLWLKPSSGSERILLKAANTHSSSQLCEQQSVHLGGVFELQAGASVFVNVTEASQVIHRVGFSSFGLLKL 260
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................................................................................................................................................. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------TNF_2  PDB: B:8-146 UniProt: 122-260                                                                                                        PROSITE (1)
                PROSITE (2) ---------------------------------------------TNF_1            ------------------------------------------------------------------------------------ PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1cda B   1 GDEDPQIAAHVVSEANSNAASVLQWAKKGYYTMKSNLVMLENGKQLTVKREGLYYVYTQVTFCSNREPSSQRPFIVGLWLKPSIGSERILLKAANTHSSSQLCEQQSVHLGGVFELQAGASVFVNVTEASQVIHRVGFSSFGLLKL 146
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140      

Chain C from PDB  Type:PROTEIN  Length:146
 aligned with CD40L_MOUSE | P27548 from UniProtKB/Swiss-Prot  Length:260

    Alignment length:146
                                   124       134       144       154       164       174       184       194       204       214       224       234       244       254      
          CD40L_MOUSE   115 GDEDPQIAAHVVSEANSNAASVLQWAKKGYYTMKSNLVMLENGKQLTVKREGLYYVYTQVTFCSNREPSSQRPFIVGLWLKPSSGSERILLKAANTHSSSQLCEQQSVHLGGVFELQAGASVFVNVTEASQVIHRVGFSSFGLLKL 260
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................................................................................................................................................. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------TNF_2  PDB: C:8-146 UniProt: 122-260                                                                                                        PROSITE (1)
                PROSITE (2) ---------------------------------------------TNF_1            ------------------------------------------------------------------------------------ PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1cda C   1 GDEDPQIAAHVVSEANSNAASVLQWAKKGYYTMKSNLVMLENGKQLTVKREGLYYVYTQVTFCSNREPSSQRPFIVGLWLKPSIGSERILLKAANTHSSSQLCEQQSVHLGGVFELQAGASVFVNVTEASQVIHRVGFSSFGLLKL 146
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140      

   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 1CDA)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1CDA)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1CDA)

(-) Gene Ontology  (28, 28)

Theoretical Model(hide GO term definitions)
Chain A,B,C   (CD40L_MOUSE | P27548)
molecular function
    GO:0005174    CD40 receptor binding    Interacting selectively and non-covalently with CD40, a receptor found on the surface of all B-lymphocytes.
    GO:0005125    cytokine activity    Functions to control the survival, growth, differentiation and effector function of tissues and cells.
    GO:0005164    tumor necrosis factor receptor binding    Interacting selectively and non-covalently with the tumor necrosis factor receptor.
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:0042100    B cell proliferation    The expansion of a B cell population by cell division. Follows B cell activation.
    GO:0007257    activation of JUN kinase activity    The initiation of the activity of the inactive enzyme JUN kinase (JNK).
    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:0048305    immunoglobulin secretion    The regulated release of immunoglobulins from a B cell or plasma cell, whose mechanism includes the use of alternate polyadenylylation signals to favor the biosynthesis of secreted forms of immunoglobulin over membrane-bound immunoglobulin.
    GO:0006954    inflammatory response    The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
    GO:0045190    isotype switching    The switching of activated B cells from IgM biosynthesis to biosynthesis of other isotypes of immunoglobulin, accomplished through a recombination process involving an intrachromosomal deletion involving switch regions that reside 5' of each constant region gene segment in the immunoglobulin heavy chain locus.
    GO:0043066    negative regulation of apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
    GO:0030168    platelet activation    A series of progressive, overlapping events triggered by exposure of the platelets to subendothelial tissue. These events include shape change, adhesiveness, aggregation, and release reactions. When carried through to completion, these events lead to the formation of a stable hemostatic plug.
    GO:0051092    positive regulation of NF-kappaB transcription factor activity    Any process that activates or increases the frequency, rate or extent of activity of the transcription factor NF-kappaB.
    GO:0042102    positive regulation of T cell proliferation    Any process that activates or increases the rate or extent of T cell proliferation.
    GO:2000353    positive regulation of endothelial cell apoptotic process    Any process that activates or increases the frequency, rate or extent of endothelial cell apoptotic process.
    GO:0032733    positive regulation of interleukin-10 production    Any process that activates or increases the frequency, rate, or extent of interleukin-10 production.
    GO:0032735    positive regulation of interleukin-12 production    Any process that activates or increases the frequency, rate, or extent of interleukin-12 production.
    GO:0032753    positive regulation of interleukin-4 production    Any process that activates or increases the frequency, rate, or extent of interleukin-4 production.
    GO:0051023    regulation of immunoglobulin secretion    Any process that modulates the frequency, rate or extent of the regulated release of immunoglobulins from a cell.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
cellular component
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    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:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    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:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    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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