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(-) Description

Title :  MOLECULAR BASIS FOR CD40 SIGNALING MEDIATED BY TRAF3
 
Authors :  C. -Z. Ni, K. Welsh, E. Leo, C. -K. Chiou, H. Wu, J. C. Reed, K. R. Ely
Date :  14 Aug 00  (Deposition) - 18 Oct 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.50
Chains :  Asym. Unit :  A,B,X,Y
Biol. Unit 1:  A,X  (1x)
Biol. Unit 2:  B,Y  (1x)
Biol. Unit 3:  B,Y  (3x)
Keywords :  Traf3 With Cd40 Peptide, Tnf Signaling, Apoptosis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Z. Ni, K. Welsh, E. Leo, C. K. Chiou, H. Wu, J. C. Reed, K. R. Ely
Molecular Basis For Cd40 Signaling Mediated By Traf3.
Proc. Natl. Acad. Sci. Usa V. 97 10395 2000
PubMed-ID: 10984535  |  Reference-DOI: 10.1073/PNAS.97.19.10395
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TNF RECEPTOR ASSOCIATED FACTOR 3
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21B
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: TRAF DOMAIN
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - B-CELL SURFACE ANTIGEN CD40
    Chains: X, Y
    Engineered: YES
    Fragment: CD40 (246-266) PEPTIDE
    Mutation: YES
    Other Details: THIS PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THIS PEPTIDE OCCURS NATURALLY IN HUMANS (HOMO SAPIENS)
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABXY
Biological Unit 1 (1x): A X 
Biological Unit 2 (1x):  B Y
Biological Unit 3 (3x):  B Y

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1FLL)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1FLL)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Trp A:424 -Pro A:425
2Trp B:424 -Pro B:425

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MATHPS50144 MATH/TRAF domain profile.TRAF3_HUMAN415-560
 		  2A:351-496
B:351-496
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MATHPS50144 MATH/TRAF domain profile.TRAF3_HUMAN415-560
 		  1A:351-496
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MATHPS50144 MATH/TRAF domain profile.TRAF3_HUMAN415-560
 		  1-
B:351-496
Biological Unit 3 (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MATHPS50144 MATH/TRAF domain profile.TRAF3_HUMAN415-560
 		  3-
B:351-496

(-) Exons   (3, 6)

Asymmetric Unit (3, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003722851aENSE00001043456chr20:44746911-44747033123TNR5_HUMAN1-17170--
1.2bENST000003722852bENSE00001798746chr20:44750459-4475053779TNR5_HUMAN18-44270--
1.3aENST000003722853aENSE00001669431chr20:44750872-44750997126TNR5_HUMAN44-86430--
1.4aENST000003722854aENSE00000662548chr20:44751249-44751395147TNR5_HUMAN86-135500--
1.4cENST000003722854cENSE00000662549chr20:44751765-4475185894TNR5_HUMAN135-166320--
1.5bENST000003722855bENSE00001615165chr20:44755279-4475534062TNR5_HUMAN166-187220--
1.5eENST000003722855eENSE00001731973chr20:44756777-4475686387TNR5_HUMAN187-216300--
1.6aENST000003722856aENSE00001670028chr20:44756969-4475699729TNR5_HUMAN216-225100--
1.6eENST000003722856eENSE00001944254chr20:44757521-44758502982TNR5_HUMAN226-277522X:246-266
Y:246-266		21
21
2.1ENST000003927451ENSE00001452921chr14:103243816-103244012197TRAF3_HUMAN-00--
2.2ENST000003927452ENSE00001512975chr14:103296671-103296809139TRAF3_HUMAN-00--
2.3ENST000003927453ENSE00001026101chr14:103336522-103336783262TRAF3_HUMAN1-82820--
2.4ENST000003927454ENSE00000660513chr14:103338254-10333830552TRAF3_HUMAN82-99180--
2.5ENST000003927455ENSE00000660514chr14:103341961-103342065105TRAF3_HUMAN100-134350--
2.6ENST000003927456ENSE00000660515chr14:103342695-103342862168TRAF3_HUMAN135-190560--
2.7ENST000003927457ENSE00000660516chr14:103352526-10335260681TRAF3_HUMAN191-217270--
2.8ENST000003927458ENSE00000660517chr14:103355897-10335597175TRAF3_HUMAN218-242250--
2.9ENST000003927459ENSE00000660518chr14:103357662-10335775493TRAF3_HUMAN243-273310--
2.10ENST0000039274510ENSE00000660519chr14:103363598-103363738141TRAF3_HUMAN274-320470--
2.11ENST0000039274511ENSE00000660520chr14:103369592-103369766175TRAF3_HUMAN321-379592A:300-315
B:300-315		16
16
2.12ENST0000039274512ENSE00001152460chr14:103371550-1033726281079TRAF3_HUMAN379-5681902A:315-504
B:315-504		190
190

(-) Sequences/Alignments

Asymmetric 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:205
 aligned with TRAF3_HUMAN | Q13114 from UniProtKB/Swiss-Prot  Length:568

    Alignment length:205
                                   373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563     
          TRAF3_HUMAN   364 LESVDKSAGQVARNTGLLESQLSRHDQMLSVHDIRLADMDLRFQVLETASYNGVLIWKIRDYKRRKQEAVMGKTLSLYSQPFYTGYFGYKMCARVYLNGDGMGKGTHLSLFFVIMRGEYDALLPWPFKQKVTLMLMDQGSSRRHLGDAFKPDPNSSSFKKPTGEMNIASGCPVFVAQTVLENGTYIKDDTIFIKVIVDTSDLPDP 568
               SCOP domains d1flla2 A:300-349 TRAF3                           d1flla1 A:350-504 TNF receptor associated factor 3 (TRAF3)                                                                                                  SCOP domains
               CATH domains 1fllA00 A:300-504 Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A                                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeeeehhhhhh..........ee..............eeee...........eeeee...................eeeee........eee.......................eeeeehhhhhh........eeeeeee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------MATH  PDB: A:351-496 UniProt: 415-560                                                                                                             -------- PROSITE
           Transcript 2 (1) Exon 2.11       --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 2 (1)
           Transcript 2 (2) ---------------Exon 2.12  PDB: A:315-504 UniProt: 379-568                                                                                                                                                     Transcript 2 (2)
                 1fll A 300 LESVDKSAGQVARNTGLLESQLSRHDQMLSVHDIRLADMDLRFQVLETASYNGVLIWKIRDYKRRKQEAVMGKTLSLYSQPFYTGYFGYKMCARVYLNGDGMGKGTHLSLFFVIMRGEYDALLPWPFKQKVTLMLMDQGSSRRHLGDAFKPDPNSSSFKKPTGEMNIASGCPVFVAQTVLENGTYIKDDTIFIKVIVDTSDLPDP 504
                                   309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499     


Chain B from PDB  Type:PROTEIN  Length:205
 aligned with TRAF3_HUMAN | Q13114 from UniProtKB/Swiss-Prot  Length:568

    Alignment length:205
                                   373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563     
          TRAF3_HUMAN   364 LESVDKSAGQVARNTGLLESQLSRHDQMLSVHDIRLADMDLRFQVLETASYNGVLIWKIRDYKRRKQEAVMGKTLSLYSQPFYTGYFGYKMCARVYLNGDGMGKGTHLSLFFVIMRGEYDALLPWPFKQKVTLMLMDQGSSRRHLGDAFKPDPNSSSFKKPTGEMNIASGCPVFVAQTVLENGTYIKDDTIFIKVIVDTSDLPDP 568
               SCOP domains d1fllb2 B:300-349 TRAF3                           d1fllb1 B:350-504 TNF receptor associated factor 3 (TRAF3)                                                                                                  SCOP domains
               CATH domains 1fllB00 B:300-504 Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A                                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eeeeehhhhhhhhhhh.....ee...........ee..eee............ee...ee...hhhhh........eeeee........eeee...........................hhhhhhh.......eeeee........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------MATH  PDB: B:351-496 UniProt: 415-560                                                                                                             -------- PROSITE
           Transcript 2 (1) Exon 2.11       --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 2 (1)
           Transcript 2 (2) ---------------Exon 2.12  PDB: B:315-504 UniProt: 379-568                                                                                                                                                     Transcript 2 (2)
                 1fll B 300 LESVDKSAGQVARNTGLLESQLSRHDQMLSVHDIRLADMDLRFQVLETASYNGVLIWKIRDYKRRKQEAVMGKTLSLYSQPFYTGYFGYKMCARVYLNGDGMGKGTHLSLFFVIMRGEYDALLPWPFKQKVTLMLMDQGSSRRHLGDAFKPDPNSSSFKKPTGEMNIASGCPVFVAQTVLENGTYIKDDTIFIKVIVDTSDLPDP 504
                                   309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499     


Chain X from PDB  Type:PROTEIN  Length:21
 aligned with TNR5_HUMAN | P25942 from UniProtKB/Swiss-Prot  Length:277

    Alignment length:21
                                   255       265 
           TNR5_HUMAN   246 NTAAPVQETLHGCQPVTQEDG 266
               SCOP domains --------------------- SCOP domains
               CATH domains --------------------- CATH domains
               Pfam domains --------------------- Pfam domains
         Sec.struct. author ..................... Sec.struct. author
                 SAPs(SNPs) --------------------- SAPs(SNPs)
                    PROSITE --------------------- PROSITE
               Transcript 1 Exon 1.6e             Transcript 1
                 1fll X 246 KTAAPVQETLHGSQPVTQEDG 266
                                   255       265 


Chain Y from PDB  Type:PROTEIN  Length:21
 aligned with TNR5_HUMAN | P25942 from UniProtKB/Swiss-Prot  Length:277

    Alignment length:21
                                   255       265 
           TNR5_HUMAN   246 NTAAPVQETLHGCQPVTQEDG 266
               SCOP domains --------------------- SCOP domains
               CATH domains --------------------- CATH domains
               Pfam domains --------------------- Pfam domains
         Sec.struct. author ..................... Sec.struct. author
                 SAPs(SNPs) --------------------- SAPs(SNPs)
                    PROSITE --------------------- PROSITE
               Transcript 1 Exon 1.6e             Transcript 1
                 1fll Y 246 KTAAPVQETLHGSQPVTQEDG 266
                                   255       265
   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  (2, 4)

Asymmetric Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Coiled coil proteins (689)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (77, 84)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (TRAF3_HUMAN | Q13114)
molecular function
    GO:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    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).
    GO:0019901    protein kinase binding    Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
    GO:0019903    protein phosphatase binding    Interacting selectively and non-covalently with any protein phosphatase.
    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:0031996    thioesterase binding    Interacting selectively and non-covalently with any thioesterase enzyme.
    GO:0005164    tumor necrosis factor receptor binding    Interacting selectively and non-covalently with the tumor necrosis factor receptor.
    GO:0031625    ubiquitin protein ligase binding    Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins.
    GO:0004842    ubiquitin-protein transferase activity    Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y --> Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0035666    TRIF-dependent toll-like receptor signaling pathway    Any series of molecular signals generated as a consequence of binding to a toll-like receptor where the TRIF adaptor mediates transduction of the signal. Toll-like receptors directly bind pattern motifs from a variety of microbial sources to initiate innate immune response.
    GO:0008063    Toll signaling pathway    A series of molecular signals initiated by the binding of an extracellular ligand to the receptor Toll on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    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:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    GO:0032088    negative regulation of NF-kappaB transcription factor activity    Any process that stops, prevents, or reduces the frequency, rate or extent of the activity of the transcription factor NF-kappaB.
    GO:0032480    negative regulation of type I interferon production    Any process that stops, prevents, or reduces the frequency, rate, or extent of type I interferon production. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families.
    GO:0016567    protein ubiquitination    The process in which one or more ubiquitin groups are added to a protein.
    GO:0042981    regulation of apoptotic process    Any process that modulates the occurrence or rate of cell death by apoptotic process.
    GO:0001817    regulation of cytokine production    Any process that modulates the frequency, rate, or extent of production of a cytokine.
    GO:0050688    regulation of defense response to virus    Any process that modulates the frequency, rate or extent of the antiviral response of a cell or organism.
    GO:0032648    regulation of interferon-beta production    Any process that modulates the frequency, rate, or extent of interferon-beta production.
    GO:0030162    regulation of proteolysis    Any process that modulates the frequency, rate or extent of the hydrolysis of a peptide bond or bonds within a protein.
    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.
    GO:0002224    toll-like receptor signaling pathway    Any series of molecular signals generated as a consequence of binding to a toll-like receptor. Toll-like receptors directly bind pattern motifs from a variety of microbial sources to initiate innate immune response.
    GO:0033209    tumor necrosis factor-mediated signaling pathway    A series of molecular signals initiated by the binding of a tumor necrosis factor to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
cellular component
    GO:0035631    CD40 receptor complex    A protein complex that contains at least CD40 (a cell surface receptor of the tumour necrosis factor receptor (TNFR) superfamily), and other signaling molecules.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0009898    cytoplasmic side of plasma membrane    The leaflet the plasma membrane that faces the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005768    endosome    A vacuole to which materials ingested by endocytosis are delivered.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

Chain X,Y   (TNR5_HUMAN | P25942)
molecular function
    GO:0003823    antigen binding    Interacting selectively and non-covalently with an antigen, any substance which is capable of inducing a specific immune response and of reacting with the products of that response, the specific antibody or specifically sensitized T-lymphocytes, or both. Binding may counteract the biological activity of the antigen.
    GO:0019899    enzyme binding    Interacting selectively and non-covalently with any enzyme.
    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:0004872    receptor activity    Combining with an extracellular or intracellular messenger to initiate a change in cell activity.
    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:0005031    tumor necrosis factor-activated receptor activity    Combining with tumor necrosis factor, a proinflammatory cytokine produced by monocytes and macrophages, to initiate a change in cell function.
    GO:0031625    ubiquitin protein ligase binding    Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins.
biological process
    GO:0042113    B cell activation    The change in morphology and behavior of a mature or immature B cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific.
    GO:0042100    B cell proliferation    The expansion of a B cell population by cell division. Follows B cell activation.
    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:0006874    cellular calcium ion homeostasis    Any process involved in the maintenance of an internal steady state of calcium ions at the level of a cell.
    GO:0071222    cellular response to lipopolysaccharide    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
    GO:0071260    cellular response to mechanical stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a mechanical stimulus.
    GO:0042832    defense response to protozoan    Reactions triggered in response to the presence of a protozoan that act to protect the cell or organism.
    GO:0051607    defense response to virus    Reactions triggered in response to the presence of a virus that act to protect the cell or organism.
    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:0002768    immune response-regulating cell surface receptor signaling pathway    A series of molecular signals initiated by the binding of an extracellular ligand to a receptor on the surface of the target cell capable of activating, perpetuating, or inhibiting an immune response.
    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: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:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    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:0030890    positive regulation of B cell proliferation    Any process that activates or increases the rate or extent of B cell proliferation.
    GO:0043547    positive regulation of GTPase activity    Any process that activates or increases the activity of a GTPase.
    GO:0043123    positive regulation of I-kappaB kinase/NF-kappaB signaling    Any process that activates or increases the frequency, rate or extent of I-kappaB kinase/NF-kappaB signaling.
    GO:0043406    positive regulation of MAP kinase activity    Any process that activates or increases the frequency, rate or extent of MAP kinase activity.
    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: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:0032735    positive regulation of interleukin-12 production    Any process that activates or increases the frequency, rate, or extent of interleukin-12 production.
    GO:0048304    positive regulation of isotype switching to IgG isotypes    Any process that activates or increases the frequency, rate or extent of isotype switching to IgG isotypes.
    GO:0090037    positive regulation of protein kinase C signaling    Any process that increases the frequency, rate, or extent of a series of reactions, mediated by the intracellular serine/threonine kinase protein kinase C, which occurs as a result of a single trigger reaction or compound.
    GO:0001934    positive regulation of protein phosphorylation    Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to amino acids within a protein.
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0006461    protein complex assembly    The aggregation, arrangement and bonding together of a set of components to form a protein complex.
    GO:0043491    protein kinase B signaling    A series of reactions, mediated by the intracellular serine/threonine kinase protein kinase B (also called AKT), which occurs as a result of a single trigger reaction or compound.
    GO:0042127    regulation of cell proliferation    Any process that modulates the frequency, rate or extent of cell proliferation.
    GO:0050776    regulation of immune response    Any process that modulates the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.
    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:0032496    response to lipopolysaccharide    Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
    GO:0033209    tumor necrosis factor-mediated signaling pathway    A series of molecular signals initiated by the binding of a tumor necrosis factor to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
cellular component
    GO:0035631    CD40 receptor complex    A protein complex that contains at least CD40 (a cell surface receptor of the tumour necrosis factor receptor (TNFR) superfamily), and other signaling molecules.
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    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: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: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:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma 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)

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        TNR5_HUMAN | P25942: 1cdf 1czz 1d00 1lb6 3qd6 5dmi 5dmj 5ihl
        TRAF3_HUMAN | Q13114: 1flk 1kzz 1l0a 1rf3 1zms 2ecy 2gkw

(-) Related Entries Specified in the PDB File

1flk