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Signaling protein
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PDB id
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1qsc
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Contents |
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* Residue conservation analysis
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PDB id:
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| Name: |
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Signaling protein
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Title:
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Crystal structure of the traf domain of traf2 in a complex with a peptide from the cd40 receptor
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Structure:
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Tnf receptor associated factor 2. Chain: a, b, c. Fragment: traf domain. Synonym: traf2. Engineered: yes. Cd40 receptor. Chain: d, e, f. Fragment: traf binding peptide. Engineered: yes.
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Source:
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Homo sapiens. Human. Organism_taxid: 9606. Expressed in: spodoptera frugiperda. Expression_system_taxid: 7108. Synthetic: yes. Other_details: sequence derived from human cd40
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Biol. unit:
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Trimer (from PDB file)
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Resolution:
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2.40Å
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R-factor:
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0.215
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R-free:
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0.257
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Authors:
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S.M.Mcwhirter,S.S.Pullen,J.M.Holton,J.J.Crute,M.R.Kehry, T.Alber
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Key ref:
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S.M.McWhirter
et al.
(1999).
Crystallographic analysis of CD40 recognition and signaling by human TRAF2.
Proc Natl Acad Sci U S A,
96,
8408-8413.
PubMed id:
DOI:
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Date:
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20-Jun-99
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Release date:
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01-Aug-99
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PROCHECK
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Headers
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References
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Q12933
(TRAF2_HUMAN) -
TNF receptor-associated factor 2
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Seq:
Struc:
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501 a.a.
179 a.a.
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Key: |
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PfamA domain |
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Secondary structure |
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CATH domain |
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DOI no:
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Proc Natl Acad Sci U S A
96:8408-8413
(1999)
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PubMed id:
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| |
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Crystallographic analysis of CD40 recognition and signaling by human TRAF2.
|
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S.M.McWhirter,
S.S.Pullen,
J.M.Holton,
J.J.Crute,
M.R.Kehry,
T.Alber.
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ABSTRACT
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Tumor necrosis factor receptor superfamily members convey signals that promote
diverse cellular responses. Receptor trimerization by extracellular ligands
initiates signaling by recruiting members of the tumor necrosis factor
receptor-associated factor (TRAF) family of adapter proteins to the receptor
cytoplasmic domains. We report the 2.4-A crystal structure of a 22-kDa,
receptor-binding fragment of TRAF2 complexed with a functionally defined peptide
from the cytoplasmic domain of the CD40 receptor. TRAF2 forms a mushroom-shaped
trimer consisting of a coiled coil and a unique beta-sandwich domain. Both
domains mediate trimerization. The CD40 peptide binds in an extended
conformation with every side chain in contact with a complementary groove on the
rim of each TRAF monomer. The spacing between the CD40 binding sites on TRAF2
supports an elegant signaling mechanism in which trimeric, extracellular ligands
preorganize the receptors to simultaneously recognize three sites on the TRAF
trimer.
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Selected figure(s)
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Figure 1.
Fig. 1. Three-dimensional structure of the TRAF-CD40-p1
complex. TRAF2-311 forms a trimer (blue, yellow, and green
ribbons), and the CD40-p1 peptides (space-filling; atom colors)
bind to the rim of all three TRAF2 monomers. TRAF-N domain
sequences form a parallel coiled coil, followed by the TRAF-C
domain, which adopts a topologically unique  -sandwich.
(A) View along the trimer axis with the coiled coil in the
front. The side chains of the conserved TrpLysIle motif
implicated in recruitment of NF-  B inducing
kinase, NIK (23), are shown in orange. The CD40 peptides are
 38 Å
from the trimer axis and 54 Å
from each other. (B) Side view with the trimer axis vertical.
The helix  2 is on the
underside of the C domain, and the C terminus is at the top.
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Figure 3.
Fig. 3. Receptor recognition by TRAF2. (A) Refined model
of CD40-p1 (Tyr-249-Thr-254) superimposed on the
solvent-flattened, MAD-phased, 2.4-Å-resolution electron
density map (1  ). (B)
Stereo view of the TRAF2-CD40-p1 contacts. The TRAF2 backbone is
depicted with ribbons. Side chains of TRAF2 residues positioned
to make hydrogen bonds to CD40-p1 are shown in purple. The
serine tongs, in which conserved serines 453-455 form hydrogen
bonds with CD40 Gln-252, are shown at the upper right. CD40
Glu-253 is at the bottom, within hydrogen-bonding distance of
TRAF2 Arg-393 and Tyr-395. CD40 Thr-254 is within
hydrogen-bonding distance of the conserved Asp-399. Primes (')
denote CD40 residues. (C) CD40-p1 (stick model) shown on the
solvent accessible surface of TRAF2 colored by electrostatic
potential (  8 to +8
kT/e; blue, positive; white, neutral; and red, negative). The
side chains of CD40 Pro-250 and Ile-251 contact a hydrophobic
region of the binding cleft, and the remaining CD40 side chains
make polar or charged interactions. (D) Comparison of CD-40-p1
(orange) and TNF-R2 (light blue) bound to TRAF2 (CD40-p1
complex, gray; TNF-R2 complex, blue). Single letters denote the
residues in CD40-TNF-R2. Three residues in the TNF-R2 peptide
not present in CD40-p1 were omitted. The TRAF2 C domains in the
two complexes were superimposed without reference to the
receptor peptides. TRAF2 adopts similar conformations in the two
complexes. The two receptor sequences make distinct side-chain
contacts.
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Figures were
selected
by the author.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
|
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H.Walden
(2010).
Selenium incorporation using recombinant techniques.
|
| |
Acta Crystallogr D Biol Crystallogr, 66,
352-357.
|
|
|
|
|
|
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P.D.Mace,
and
S.J.Riedl
(2010).
Molecular cell death platforms and assemblies.
|
| |
Curr Opin Cell Biol, 22,
828-836.
|
|
|
|
|
|
|
S.G.Hymowitz,
and
V.M.Dixit
(2010).
Unleashing cell death: the Fas-FADD complex.
|
| |
Nat Struct Mol Biol, 17,
1289-1290.
|
|
|
|
|
|
|
S.K.Manna,
B.Babajan,
P.B.Raghavendra,
N.Raviprakash,
and
C.Sureshkumar
(2010).
Inhibiting TRAF2-mediated activation of NF-kappaB facilitates induction of AP-1.
|
| |
J Biol Chem, 285,
11617-11627.
|
|
|
|
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|
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H.H.Jabara,
Y.Weng,
T.Sannikova,
and
R.S.Geha
(2009).
TRAF2 and TRAF3 independently mediate Ig class switching driven by CD40.
|
| |
Int Immunol, 21,
477-488.
|
|
|
|
|
|
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Q.Yin,
B.Lamothe,
B.G.Darnay,
and
H.Wu
(2009).
Structural basis for the lack of E2 interaction in the RING domain of TRAF2.
|
| |
Biochemistry, 48,
10558-10567.
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PDB code:
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|
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Q.Yin,
S.C.Lin,
B.Lamothe,
M.Lu,
Y.C.Lo,
G.Hura,
L.Zheng,
R.L.Rich,
A.D.Campos,
D.G.Myszka,
M.J.Lenardo,
B.G.Darnay,
and
H.Wu
(2009).
E2 interaction and dimerization in the crystal structure of TRAF6.
|
| |
Nat Struct Mol Biol, 16,
658-666.
|
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PDB codes:
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|
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R.Elgueta,
M.J.Benson,
V.C.de Vries,
A.Wasiuk,
Y.Guo,
and
R.J.Noelle
(2009).
Molecular mechanism and function of CD40/CD40L engagement in the immune system.
|
| |
Immunol Rev, 229,
152-172.
|
|
|
|
|
|
|
T.A.Wassenaar,
W.J.Quax,
and
A.E.Mark
(2008).
The conformation of the extracellular binding domain of Death Receptor 5 in the presence and absence of the activating ligand TRAIL: a molecular dynamics study.
|
| |
Proteins, 70,
333-343.
|
|
|
|
|
|
|
W.Chadwick,
T.Magnus,
B.Martin,
A.Keselman,
M.P.Mattson,
and
S.Maudsley
(2008).
Targeting TNF-alpha receptors for neurotherapeutics.
|
| |
Trends Neurosci, 31,
504-511.
|
|
|
|
|
|
|
B.S.Hostager
(2007).
Roles of TRAF6 in CD40 signaling.
|
| |
Immunol Res, 39,
105-114.
|
|
|
|
|
|
|
C.N.Cronin,
K.B.Lim,
and
J.Rogers
(2007).
Production of selenomethionyl-derivatized proteins in baculovirus-infected insect cells.
|
| |
Protein Sci, 16,
2023-2029.
|
|
|
|
|
|
|
F.K.Chan
(2007).
Three is better than one: pre-ligand receptor assembly in the regulation of TNF receptor signaling.
|
| |
Cytokine, 37,
101-107.
|
|
|
|
|
|
|
E.R.Sprague,
C.Wang,
D.Baker,
and
P.J.Bjorkman
(2006).
Crystal structure of the HSV-1 Fc receptor bound to Fc reveals a mechanism for antibody bipolar bridging.
|
| |
PLoS Biol, 4,
e148.
|
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PDB codes:
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J.H.Thomas
(2006).
Analysis of homologous gene clusters in Caenorhabditis elegans reveals striking regional cluster domains.
|
| |
Genetics, 172,
127-143.
|
|
|
|
|
|
|
J.H.Thomas
(2006).
Adaptive evolution in two large families of ubiquitin-ligase adapters in nematodes and plants.
|
| |
Genome Res, 16,
1017-1030.
|
|
|
|
|
|
|
K.H.Szymczyk,
T.A.Freeman,
C.S.Adams,
V.Srinivas,
and
M.J.Steinbeck
(2006).
Active caspase-3 is required for osteoclast differentiation.
|
| |
J Cell Physiol, 209,
836-844.
|
|
|
|
|
|
|
C.B.Carlson,
D.A.Bernstein,
D.S.Annis,
T.M.Misenheimer,
B.L.Hannah,
D.F.Mosher,
and
J.L.Keck
(2005).
Structure of the calcium-rich signature domain of human thrombospondin-2.
|
| |
Nat Struct Mol Biol, 12,
910-914.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
H.Xu,
C.Yang,
L.Chen,
I.A.Kataeva,
W.Tempel,
D.Lee,
J.E.Habel,
D.Nguyen,
J.W.Pflugrath,
J.D.Ferrara,
W.B.Arendall,
J.S.Richardson,
D.C.Richardson,
Z.J.Liu,
M.G.Newton,
J.P.Rose,
and
B.C.Wang
(2005).
Away from the edge II: in-house Se-SAS phasing with chromium radiation.
|
| |
Acta Crystallogr D Biol Crystallogr, 61,
960-966.
|
|
|
PDB code:
|
|
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|
|
|
|
|
J.Hauer,
S.Püschner,
P.Ramakrishnan,
U.Simon,
M.Bongers,
C.Federle,
and
H.Engelmann
(2005).
TNF receptor (TNFR)-associated factor (TRAF) 3 serves as an inhibitor of TRAF2/5-mediated activation of the noncanonical NF-kappaB pathway by TRAF-binding TNFRs.
|
| |
Proc Natl Acad Sci U S A, 102,
2874-2879.
|
|
|
|
|
|
|
K.Kanazawa,
and
A.Kudo
(2005).
Self-assembled RANK induces osteoclastogenesis ligand-independently.
|
| |
J Bone Miner Res, 20,
2053-2060.
|
|
|
|
|
|
|
P.D.Laible,
A.N.Hata,
A.E.Crawford,
and
D.K.Hanson
(2005).
Incorporation of selenomethionine into induced intracytoplasmic membrane proteins of Rhodobacter species.
|
| |
J Struct Funct Genomics, 6,
95.
|
|
|
|
|
|
|
V.Saridakis,
Y.Sheng,
F.Sarkari,
M.N.Holowaty,
K.Shire,
T.Nguyen,
R.G.Zhang,
J.Liao,
W.Lee,
A.M.Edwards,
C.H.Arrowsmith,
and
L.Frappier
(2005).
Structure of the p53 binding domain of HAUSP/USP7 bound to Epstein-Barr nuclear antigen 1 implications for EBV-mediated immortalization.
|
| |
Mol Cell, 18,
25-36.
|
|
|
PDB codes:
|
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|
|
|
|
|
|
G.A.Bishop
(2004).
The multifaceted roles of TRAFs in the regulation of B-cell function.
|
| |
Nat Rev Immunol, 4,
775-786.
|
|
|
|
|
|
|
J.Holton,
and
T.Alber
(2004).
Automated protein crystal structure determination using ELVES.
|
| |
Proc Natl Acad Sci U S A, 101,
1537-1542.
|
|
|
PDB codes:
|
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|
|
|
|
|
|
K.Saito,
T.Kigawa,
S.Koshiba,
K.Sato,
Y.Matsuo,
A.Sakamoto,
T.Takagi,
M.Shirouzu,
T.Yabuki,
E.Nunokawa,
E.Seki,
T.Matsuda,
M.Aoki,
Y.Miyata,
N.Hirakawa,
M.Inoue,
T.Terada,
T.Nagase,
R.Kikuno,
M.Nakayama,
O.Ohara,
A.Tanaka,
and
S.Yokoyama
(2004).
The CAP-Gly domain of CYLD associates with the proline-rich sequence in NEMO/IKKgamma.
|
| |
Structure, 12,
1719-1728.
|
|
|
PDB code:
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J.M.Zapata
(2003).
TNF-receptor-associated factors as targets for drug development.
|
| |
Expert Opin Ther Targets, 7,
411-425.
|
|
|
|
|
|
|
K.Pfeffer
(2003).
Biological functions of tumor necrosis factor cytokines and their receptors.
|
| |
Cytokine Growth Factor Rev, 14,
185-191.
|
|
|
|
|
|
|
L.He,
D.P.Olson,
X.Wu,
T.S.Karpova,
J.G.McNally,
and
P.E.Lipsky
(2003).
A flow cytometric method to detect protein-protein interaction in living cells by directly visualizing donor fluorophore quenching during CFP-->YFP fluorescence resonance energy transfer (FRET).
|
| |
Cytometry A, 55,
71-85.
|
|
|
|
|
|
|
M.L.Quillin,
and
B.W.Matthews
(2003).
Selling candles in a post-Edison world: phasing with noble gases bound within engineered sites.
|
| |
Acta Crystallogr D Biol Crystallogr, 59,
1930-1934.
|
|
|
|
|
|
|
P.W.Dempsey,
S.E.Doyle,
J.Q.He,
and
G.Cheng
(2003).
The signaling adaptors and pathways activated by TNF superfamily.
|
| |
Cytokine Growth Factor Rev, 14,
193-209.
|
|
|
|
|
|
|
S.M.Soond,
J.L.Terry,
J.D.Colbert,
and
D.W.Riches
(2003).
TRUSS, a novel tumor necrosis factor receptor 1 scaffolding protein that mediates activation of the transcription factor NF-kappaB.
|
| |
Mol Cell Biol, 23,
8334-8344.
|
|
|
|
|
|
|
W.F.Coffin,
T.R.Geiger,
and
J.M.Martin
(2003).
Transmembrane domains 1 and 2 of the latent membrane protein 1 of Epstein-Barr virus contain a lipid raft targeting signal and play a critical role in cytostasis.
|
| |
J Virol, 77,
3749-3758.
|
|
|
|
|
|
|
C.Li,
C.Z.Ni,
M.L.Havert,
E.Cabezas,
J.He,
D.Kaiser,
J.C.Reed,
A.C.Satterthwait,
G.Cheng,
and
K.R.Ely
(2002).
Downstream regulator TANK binds to the CD40 recognition site on TRAF3.
|
| |
Structure, 10,
403-411.
|
|
|
PDB codes:
|
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|
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C.Z.Ni,
K.Welsh,
J.Zheng,
M.Havert,
J.C.Reed,
and
K.R.Ely
(2002).
Crystallization and preliminary X-ray analysis of the TRAF domain of TRAF3.
|
| |
Acta Crystallogr D Biol Crystallogr, 58,
1340-1342.
|
|
|
|
|
|
|
G.Polekhina,
C.M.House,
N.Traficante,
J.P.Mackay,
F.Relaix,
D.A.Sassoon,
M.W.Parker,
and
D.D.Bowtell
(2002).
Siah ubiquitin ligase is structurally related to TRAF and modulates TNF-alpha signaling.
|
| |
Nat Struct Biol, 9,
68-75.
|
|
|
PDB code:
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|
|
|
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|
|
H.Glauner,
D.Siegmund,
H.Motejadded,
P.Scheurich,
F.Henkler,
O.Janssen,
and
H.Wajant
(2002).
Intracellular localization and transcriptional regulation of tumor necrosis factor (TNF) receptor-associated factor 4 (TRAF4).
|
| |
Eur J Biochem, 269,
4819-4829.
|
|
|
|
|
|
|
H.Ye,
J.R.Arron,
B.Lamothe,
M.Cirilli,
T.Kobayashi,
N.K.Shevde,
D.Segal,
O.K.Dzivenu,
M.Vologodskaia,
M.Yim,
K.Du,
S.Singh,
J.W.Pike,
B.G.Darnay,
Y.Choi,
and
H.Wu
(2002).
Distinct molecular mechanism for initiating TRAF6 signalling.
|
| |
Nature, 418,
443-447.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
J.C.Reed,
and
K.R.Ely
(2002).
Degrading liaisons: Siah structure revealed.
|
| |
Nat Struct Biol, 9,
8.
|
|
|
|
|
|
|
J.R.Arron,
Y.Pewzner-Jung,
M.C.Walsh,
T.Kobayashi,
and
Y.Choi
(2002).
Regulation of the subcellular localization of tumor necrosis factor receptor-associated factor (TRAF)2 by TRAF1 reveals mechanisms of TRAF2 signaling.
|
| |
J Exp Med, 196,
923-934.
|
|
|
|
|
|
|
K.R.Ely,
and
C.Li
(2002).
Structurally adaptive hot spots at a protein interaction interface on TRAF3.
|
| |
J Mol Recognit, 15,
286-290.
|
|
|
|
|
|
|
O.V.Moroz,
A.A.Antson,
E.J.Dodson,
H.J.Burrell,
S.J.Grist,
R.M.Lloyd,
N.J.Maitland,
G.G.Dodson,
K.S.Wilson,
E.Lukanidin,
and
I.B.Bronstein
(2002).
The structure of S100A12 in a hexameric form and its proposed role in receptor signalling.
|
| |
Acta Crystallogr D Biol Crystallogr, 58,
407-413.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
A.Kaykas,
K.Worringer,
and
B.Sugden
(2001).
CD40 and LMP-1 both signal from lipid rafts but LMP-1 assembles a distinct, more efficient signaling complex.
|
| |
EMBO J, 20,
2641-2654.
|
|
|
|
|
|
|
E.M.Gravallese,
D.L.Galson,
S.R.Goldring,
and
P.E.Auron
(2001).
The role of TNF-receptor family members and other TRAF-dependent receptors in bone resorption.
|
| |
Arthritis Res, 3,
6.
|
|
|
|
|
|
|
N.Kobayashi,
Y.Kadono,
A.Naito,
K.Matsumoto,
T.Yamamoto,
S.Tanaka,
and
J.Inoue
(2001).
Segregation of TRAF6-mediated signaling pathways clarifies its role in osteoclastogenesis.
|
| |
EMBO J, 20,
1271-1280.
|
|
|
|
|
|
|
R.M.Locksley,
N.Killeen,
and
M.J.Lenardo
(2001).
The TNF and TNF receptor superfamilies: integrating mammalian biology.
|
| |
Cell, 104,
487-501.
|
|
|
|
|
|
|
A.G.Eliopoulos,
C.Davies,
P.G.Knox,
N.J.Gallagher,
S.C.Afford,
D.H.Adams,
and
L.S.Young
(2000).
CD40 induces apoptosis in carcinoma cells through activation of cytotoxic ligands of the tumor necrosis factor superfamily.
|
| |
Mol Cell Biol, 20,
5503-5515.
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C.Z.Ni,
K.Welsh,
E.Leo,
C.K.Chiou,
H.Wu,
J.C.Reed,
and
K.R.Ely
(2000).
Molecular basis for CD40 signaling mediated by TRAF3.
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Proc Natl Acad Sci U S A, 97,
10395-10399.
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PDB codes:
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D.H.Tsao,
T.McDonagh,
J.B.Telliez,
S.Hsu,
K.Malakian,
G.Y.Xu,
and
L.L.Lin
(2000).
Solution structure of N-TRADD and characterization of the interaction of N-TRADD and C-TRAF2, a key step in the TNFR1 signaling pathway.
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Mol Cell, 5,
1051-1057.
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PDB code:
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E.Y.Jones
(2000).
The tumour necrosis factor receptor family: life or death choices.
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Curr Opin Struct Biol, 10,
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H.Liu,
H.Nishitoh,
H.Ichijo,
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Activation of apoptosis signal-regulating kinase 1 (ASK1) by tumor necrosis factor receptor-associated factor 2 requires prior dissociation of the ASK1 inhibitor thioredoxin.
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Mol Cell Biol, 20,
2198-2208.
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H.T.Idriss,
and
J.H.Naismith
(2000).
TNF alpha and the TNF receptor superfamily: structure-function relationship(s).
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Microsc Res Tech, 50,
184-195.
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H.Ye,
and
H.Wu
(2000).
Thermodynamic characterization of the interaction between TRAF2 and tumor necrosis factor receptor peptides by isothermal titration calorimetry.
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Proc Natl Acad Sci U S A, 97,
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R.Schwandner,
K.Yamaguchi,
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Requirement of tumor necrosis factor receptor-associated factor (TRAF)6 in interleukin 17 signal transduction.
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J Exp Med, 191,
1233-1240.
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U.Schönbeck,
F.Mach,
and
P.Libby
(2000).
CD154 (CD40 ligand).
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Int J Biochem Cell Biol, 32,
687-693.
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Y.C.Park,
H.Ye,
C.Hsia,
D.Segal,
R.L.Rich,
H.C.Liou,
D.G.Myszka,
and
H.Wu
(2000).
A novel mechanism of TRAF signaling revealed by structural and functional analyses of the TRADD-TRAF2 interaction.
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| |
Cell, 101,
777-787.
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PDB code:
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S.G.Hymowitz,
H.W.Christinger,
G.Fuh,
M.Ultsch,
M.O'Connell,
R.F.Kelley,
A.Ashkenazi,
and
A.M.de Vos
(1999).
Triggering cell death: the crystal structure of Apo2L/TRAIL in a complex with death receptor 5.
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Mol Cell, 4,
563-571.
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PDB code:
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S.M.McWhirter,
S.S.Pullen,
B.G.Werneburg,
M.E.Labadia,
R.H.Ingraham,
J.J.Crute,
M.R.Kehry,
and
T.Alber
(1999).
Structural and biochemical analysis of signal transduction by the TRAF family of adapter proteins.
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Cold Spring Harb Symp Quant Biol, 64,
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S.S.Pullen,
M.E.Labadia,
R.H.Ingraham,
S.M.McWhirter,
D.S.Everdeen,
T.Alber,
J.J.Crute,
and
M.R.Kehry
(1999).
High-affinity interactions of tumor necrosis factor receptor-associated factors (TRAFs) and CD40 require TRAF trimerization and CD40 multimerization.
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Biochemistry, 38,
10168-10177.
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
code is
shown on the right.
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