Database Accession: DI3000007
Name: TNF receptor associated factor 2 in complex with a peptide from CD40
PDB ID: 1czz
Experimental method: X-ray (2.70 Å)
Source organism: Homo sapiens
Proof of disorder:
Primary publication of the structure:
Ye H, Park YC, Kreishman M, Kieff E, Wu H
The structural basis for the recognition of diverse receptor sequences by TRAF2.
(1999) Mol. Cell 4: 321-30
PMID: 10518213
Abstract:
Many members of the tumor necrosis factor receptor (TNFR) superfamily initiate intracellular signaling by recruiting TNFR-associated factors (TRAFs) through their cytoplasmic tails. TRAFs apparently recognize highly diverse receptor sequences. Crystal structures of the TRAF domain of human TRAF2 in complex with peptides from the TNFR family members CD40, CD30, Ox40, 4-1BB, and the EBV oncoprotein LMP1 revealed a conserved binding mode. A major TRAF2-binding consensus sequence, (P/S/A/T)x(Q/E)E, and a minor consensus motif, PxQxxD, can be defined from the structural analysis, which encompass all known TRAF2-binding sequences. The structural information provides a template for the further dissection of receptor binding specificity of TRAF2 and for the understanding of the complexity of TRAF-mediated signal transduction.
Annotations from the GeneOntology database. Only terms that fit at least two of the interacting proteins are shown. Molecular function:
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.
ubiquitin protein ligase binding Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins.
Biological process:
protein complex assembly The aggregation, arrangement and bonding together of a set of components to form a protein complex.
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.
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.
regulation of immunoglobulin secretion Any process that modulates the frequency, rate or extent of the regulated release of immunoglobulins from a cell.
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.
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.
positive regulation of cytokine production Any process that activates or increases the frequency, rate or extent of production of a cytokine.
positive regulation of lymphocyte mediated immunity Any process that activates or increases the frequency, rate, or extent of lymphocyte mediated immunity.
positive regulation of hydrolase activity Any process that activates or increases the frequency, rate or extent of hydrolase activity, the catalysis of the hydrolysis of various bonds.
intracellular signal transduction The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell.
positive regulation of MAP kinase activity Any process that activates or increases the frequency, rate or extent of MAP kinase activity.
positive regulation of lymphocyte activation Any process that activates or increases the frequency, rate or extent of lymphocyte activation.
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.
cellular response to oxygen-containing compound 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 an oxygen-containing compound stimulus.
response to nitrogen compound 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 nitrogen compound stimulus.
positive regulation of apoptotic process Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
Cellular component:
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.
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.
vesicle Any small, fluid-filled, spherical organelle enclosed by membrane.
Structural annotations of the participating protein chains.Entry contents: 4 distinct polypeptide molecules
Chains: D, A, B, C
Notes: Chain E was removed as chains A, B, C and D highlight the biologically relevant interaction.
Name: Tumor necrosis factor receptor superfamily member 5
Source organism: Homo sapiens
Length: 9 residues
Sequence:Sequence according to PDB SEQRESPVQETLHGC
UniProtKB AC: P25942 (positions: 250-258) Coverage: 3.2%
UniRef90 AC: UniRef90_P25942 (positions: 250-258)
Name: TNF receptor-associated factor 2
Source organism: Homo sapiens
Length: 187 residues
Sequence:Sequence according to PDB SEQRESEALSSKVQQLERSIGLKDLAMADLEQKVLEMEASTYDGVFIWKISDFPRKRQEAVAGRIPAIFSPAFYTSRYGYKMCLRIYLNGDGTGRGTHLSLFFVVMKGPNDALLRWPFNQKVTLMLLDQNNREHVIDAFRPDVTSSSFQRPVNDMNIASGCPLFCPVSKMEAKNSYVRDDAIFIKAIVDLTGL
UniProtKB AC: Q12933 (positions: 315-501) Coverage: 37.3%
UniRef90 AC: UniRef90_Q12933 (positions: 315-501)
Name: TNF receptor-associated factor 2
Source organism: Homo sapiens
Length: 187 residues
Sequence:Sequence according to PDB SEQRESEALSSKVQQLERSIGLKDLAMADLEQKVLEMEASTYDGVFIWKISDFPRKRQEAVAGRIPAIFSPAFYTSRYGYKMCLRIYLNGDGTGRGTHLSLFFVVMKGPNDALLRWPFNQKVTLMLLDQNNREHVIDAFRPDVTSSSFQRPVNDMNIASGCPLFCPVSKMEAKNSYVRDDAIFIKAIVDLTGL
UniProtKB AC: Q12933 (positions: 315-501) Coverage: 37.3%
UniRef90 AC: UniRef90_Q12933 (positions: 315-501)
Name: TNF receptor-associated factor 2
Source organism: Homo sapiens
Length: 187 residues
Sequence:Sequence according to PDB SEQRESEALSSKVQQLERSIGLKDLAMADLEQKVLEMEASTYDGVFIWKISDFPRKRQEAVAGRIPAIFSPAFYTSRYGYKMCLRIYLNGDGTGRGTHLSLFFVVMKGPNDALLRWPFNQKVTLMLLDQNNREHVIDAFRPDVTSSSFQRPVNDMNIASGCPLFCPVSKMEAKNSYVRDDAIFIKAIVDLTGL
UniProtKB AC: Q12933 (positions: 315-501) Coverage: 37.3%
UniRef90 AC: UniRef90_Q12933 (positions: 315-501)
Evidence demonstrating that the participating proteins are unstructured prior to the interaction and their folding is coupled to binding. Chain D:
The protein region involved in the interaction contains a known functional linear motif (LIG_TRAF2_1).
Chain A:
The MATH domain involved in the interaction is known to adopt a stable structure in isolation in trimeric form. A solved structure of the domain trimer without bound ligands is represented by PDB ID 1ca4.
Chain B:
The MATH domain involved in the interaction is known to adopt a stable structure in isolation in trimeric form. A solved structure of the domain trimer without bound ligands is represented by PDB ID 1ca4.
Chain C:
The MATH domain involved in the interaction is known to adopt a stable structure in isolation in trimeric form. A solved structure of the domain trimer without bound ligands is represented by PDB ID 1ca4.
Structures from the PDB that contain the same number of proteins, and the proteins from the two structures show a sufficient degree of pairwise similarity, i.e. they belong to the same UniRef90 cluster (the full proteins exhibit at least 90% sequence identity) and convey roughly the same region to their respective interactions (the two regions from the two proteins share a minimum of 70% overlap). The structure can be rotated by left click and hold anywhere on the structure. Representation options can be edited by right clicking on the structure window.
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