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Contents |
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210 a.a.
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221 a.a.
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75 a.a.
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76 a.a.
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* Residue conservation analysis
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PDB id:
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Immune system
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Title:
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Crystal structure of k63-specific fab apu.3a8 bound to k63-linked di- ubiquitin
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Structure:
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Human igg1 fab fragment light chain. Chain: a. Engineered: yes. Human igg1 fab fragment heavy chain. Chain: b. Engineered: yes. Ubiquitin d77. Chain: x. Engineered: yes.
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Source:
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Homo sapiens. Human. Organism_taxid: 9606. Gene: fab fragment light chain. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: protein selected by phage display. Gene: rps27a, uba80, ubcep1, uba52, ubcep2, ubb, ubc.
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Resolution:
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2.60Å
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R-factor:
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0.224
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R-free:
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0.261
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Authors:
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S.G.Hymowitz
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Key ref:
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K.Newton
et al.
(2008).
Ubiquitin chain editing revealed by polyubiquitin linkage-specific antibodies.
Cell,
134,
668-678.
PubMed id:
DOI:
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Date:
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18-Jul-08
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Release date:
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30-Sep-08
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PROCHECK
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Headers
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References
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Q6PIL8
(Q6PIL8_HUMAN) -
IGK@ protein from Homo sapiens
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Seq:
Struc:
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236 a.a.
210 a.a.*
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No UniProt id for this chain
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DOI no:
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Cell
134:668-678
(2008)
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PubMed id:
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Ubiquitin chain editing revealed by polyubiquitin linkage-specific antibodies.
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K.Newton,
M.L.Matsumoto,
I.E.Wertz,
D.S.Kirkpatrick,
J.R.Lill,
J.Tan,
D.Dugger,
N.Gordon,
S.S.Sidhu,
F.A.Fellouse,
L.Komuves,
D.M.French,
R.E.Ferrando,
C.Lam,
D.Compaan,
C.Yu,
I.Bosanac,
S.G.Hymowitz,
R.F.Kelley,
V.M.Dixit.
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ABSTRACT
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Posttranslational modification of proteins with polyubiquitin occurs in diverse
signaling pathways and is tightly regulated to ensure cellular homeostasis.
Studies employing ubiquitin mutants suggest that the fate of polyubiquitinated
proteins is determined by which lysine within ubiquitin is linked to the C
terminus of an adjacent ubiquitin. We have developed linkage-specific antibodies
that recognize polyubiquitin chains joined through lysine 63 (K63) or 48 (K48).
A cocrystal structure of an anti-K63 linkage Fab bound to K63-linked diubiquitin
provides insight into the molecular basis for specificity. We use these
antibodies to demonstrate that RIP1, which is essential for tumor necrosis
factor-induced NF-kappaB activation, and IRAK1, which participates in signaling
by interleukin-1beta and Toll-like receptors, both undergo polyubiquitin editing
in stimulated cells. Both kinase adaptors initially acquire K63-linked
polyubiquitin, while at later times K48-linked polyubiquitin targets them for
proteasomal degradation. Polyubiquitin editing may therefore be a general
mechanism for attenuating innate immune signaling.
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Selected figure(s)
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Figure 1.
Figure 1. Structural Analysis of Apu2.16 and Apu3.A8 Anti-K63
Linkage Fabs Bound to K63-Linked Diubiquitin
(A) The
complex between K63-linked diubiquitin (orange) and the Apu2.16
Fab fragment (heavy chain: green, light chain: magenta). Heavy
chain CDR3 (H3) contacts both ubiquitins on either side of the
isopeptide linkage. H3 side chains within 4.2 Å of
diubiquitin and ubiquitin side chains within 4.2 Å of H3
are shown as sticks. Residues mentioned in the text are in bold
for ubiquitin and italics for the Fab. K63 in the acceptor
ubiquitin is shown as a sphere.
(B) Comparison of K63-
(top) and K48-linked (bottom) diubiquitin. Lysine donor
ubiquitins are light orange and acceptor ubiquitins are bright
orange. K48-linked diubiquitin forms a more compact shape with
the chain extending perpendicular to the ubiquitin dimer, while
the K63-linked diubiquitin chain will extend in a more elongated
manner.
(C) Superposition of Apu2.16 (colored as in A) and
Apu3.A8 (heavy chain: light green, light chain: pink) showing
the location of the two changes in L2 (S52R) and H3 (S52T)
introduced in the affinity maturation process to create Apu3.A8.
The structural differences in L1 in the two Fabs are likely due
to crystal packing. L1 (as well as the N terminus) are in a
noncanonical conformation likely due to interactions with L3,
which has sequence and structural differences relative to the
phage library parent sequence (Figure S2).
(D) Charge
complementarity between Apu3.A8 (transparent) and diubiquitin
(solid). Electrostatic surfaces were calculated with PyMol.
Regions of positive potential are blue; regions with negative
potential are red. In the Apu3.A8 light chain, R52 (which is
introduced in Apu3.A8) and R66 contribute to a positive region
that is close to a negatively charged region on the ubiquitin
surface, created in part by residues D21, D58, and E18 from the
K63 acceptor ubiquitin.
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Figure 3.
Figure 3. Mass Spectrometry Confirms the Linkage Specificity
of Apu2.07 and Apu3.A8 in Immunoprecipitations
(A–D) BJAB
cell lysates were immunoprecipitated with Apu2.07, Apu3.A8, or
an isotype control antibody recognizing HER2. Mass spectrometry
was used to determine the total amount of ubiquitin
immunoprecipitated (A) as well as the polyubiquitin linkages in
the lysate (B) and immunoprecipitates (C and D).
(E) MuRF1
autoubiquitination reactions performed in vitro with WT, K48R,
or K63R ubiquitin were immunoprecipitated with Apu2.07, Apu3.A8,
or isotype control. Numbers in parentheses indicate the relevant
lanes and columns in (F)–(I).
(F) Autoubiquitination
reactions and immunoprecipitations depicted in (E) were western
blotted with a pan-ubiquitin antibody. The hatched red lines
indicate the portion of the gel that was cut out and subjected
to analysis by mass spectrometry.
(G–I) Mass spectrometry
was used to determine the polyubiquitin linkages in the
autoubiquitination reactions and immunoprecipitations depicted
in (E).
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The above figures are
reprinted
by permission from Cell Press:
Cell
(2008,
134,
668-678)
copyright 2008.
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Figures were
selected
by an automated process.
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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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|
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L.Feng,
and
J.Chen
(2012).
The E3 ligase RNF8 regulates KU80 removal and NHEJ repair.
|
| |
Nat Struct Mol Biol,
19,
201-206.
|
|
|
|
|
|
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Y.Kulathu,
and
D.Komander
(2012).
Atypical ubiquitylation - the unexplored world of polyubiquitin beyond Lys48 and Lys63 linkages.
|
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Nat Rev Mol Cell Biol,
13,
508-523.
|
|
|
|
|
|
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Y.Ye,
G.Blaser,
M.H.Horrocks,
M.J.Ruedas-Rama,
S.Ibrahim,
A.A.Zhukov,
A.Orte,
D.Klenerman,
S.E.Jackson,
and
D.Komander
(2012).
Ubiquitin chain conformation regulates recognition and activity of interacting proteins.
|
| |
Nature,
492,
266-270.
|
|
|
|
|
|
|
A.C.Vitari,
K.G.Leong,
K.Newton,
C.Yee,
K.O'Rourke,
J.Liu,
L.Phu,
R.Vij,
R.Ferrando,
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S.Mohan,
A.Pandita,
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I.E.Wertz,
W.Q.Gao,
D.M.French,
and
V.M.Dixit
(2011).
COP1 is a tumour suppressor that causes degradation of ETS transcription factors.
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Nature,
474,
403-406.
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A.Oberst,
and
D.R.Green
(2011).
It cuts both ways: reconciling the dual roles of caspase 8 in cell death and survival.
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| |
Nat Rev Mol Cell Biol,
12,
757-763.
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E.Argenzio,
T.Bange,
B.Oldrini,
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R.Peesari,
S.Mari,
P.P.Di Fiore,
M.Mann,
and
S.Polo
(2011).
Proteomic snapshot of the EGF-induced ubiquitin network.
|
| |
Mol Syst Biol,
7,
462.
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|
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|
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I.Bosanac,
L.Phu,
B.Pan,
I.Zilberleyb,
B.Maurer,
V.M.Dixit,
S.G.Hymowitz,
and
D.S.Kirkpatrick
(2011).
Modulation of K11-linkage formation by variable loop residues within UbcH5A.
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J Mol Biol,
408,
420-431.
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PDB code:
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K.Kuhlbrodt,
P.C.Janiesch,
E.Kevei,
A.Segref,
R.Barikbin,
and
T.Hoppe
(2011).
The Machado-Joseph disease deubiquitylase ATX-3 couples longevity and proteostasis.
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Nat Cell Biol,
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M.A.O'Donnell,
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FEBS J,
278,
877-887.
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J.J.Cooper,
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Transcription factor IIS cooperates with the E3 ligase UBR5 to ubiquitinate the CDK9 subunit of the positive transcription elongation factor B.
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J Biol Chem,
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M.Bosshard,
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U.Hübscher,
H.Meyer,
and
K.Ramadan
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The ubiquitin-selective segregase VCP/p97 orchestrates the response to DNA double-strand breaks.
|
| |
Nat Cell Biol,
13,
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|
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|
|
|
|
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P.La Rosa,
M.Marino,
and
F.Acconcia
(2011).
17β-estradiol regulates estrogen receptor α monoubiquitination.
|
| |
IUBMB Life,
63,
49-53.
|
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|
|
|
|
|
P.La Rosa,
V.Pesiri,
M.Marino,
and
F.Acconcia
(2011).
17β-Estradiol-induced cell proliferation requires estrogen receptor (ER) α monoubiquitination.
|
| |
Cell Signal,
23,
1128-1135.
|
|
|
|
|
|
|
R.Rai,
J.M.Li,
H.Zheng,
G.T.Lok,
Y.Deng,
M.S.Huen,
J.Chen,
J.Jin,
and
S.Chang
(2011).
The E3 ubiquitin ligase Rnf8 stabilizes Tpp1 to promote telomere end protection.
|
| |
Nat Struct Mol Biol,
18,
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|
|
|
|
|
|
|
S.Liu,
and
Z.J.Chen
(2011).
Expanding role of ubiquitination in NF-κB signaling.
|
| |
Cell Res,
21,
6.
|
|
|
|
|
|
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A.M.Mabb,
and
M.D.Ehlers
(2010).
Ubiquitination in postsynaptic function and plasticity.
|
| |
Annu Rev Cell Dev Biol,
26,
179-210.
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|
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|
|
A.Peth,
T.Uchiki,
and
A.L.Goldberg
(2010).
ATP-dependent steps in the binding of ubiquitin conjugates to the 26S proteasome that commit to degradation.
|
| |
Mol Cell,
40,
671-681.
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A.Vina-Vilaseca,
and
A.Sorkin
(2010).
Lysine 63-linked polyubiquitination of the dopamine transporter requires WW3 and WW4 domains of Nedd4-2 and UBE2D ubiquitin-conjugating enzymes.
|
| |
J Biol Chem,
285,
7645-7656.
|
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|
|
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|
|
B.A.Malynn,
and
A.Ma
(2010).
Ubiquitin makes its mark on immune regulation.
|
| |
Immunity,
33,
843-852.
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|
C.Marx,
J.M.Held,
B.W.Gibson,
and
C.C.Benz
(2010).
ErbB2 trafficking and degradation associated with K48 and K63 polyubiquitination.
|
| |
Cancer Res,
70,
3709-3717.
|
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|
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|
|
C.Rothenberg,
D.Srinivasan,
L.Mah,
S.Kaushik,
C.M.Peterhoff,
J.Ugolino,
S.Fang,
A.M.Cuervo,
R.A.Nixon,
and
M.J.Monteiro
(2010).
Ubiquilin functions in autophagy and is degraded by chaperone-mediated autophagy.
|
| |
Hum Mol Genet,
19,
3219-3232.
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D.E.Christofferson,
and
J.Yuan
(2010).
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| |
Curr Opin Cell Biol,
22,
263-268.
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D.J.Perkins,
N.Qureshi,
and
S.N.Vogel
(2010).
A Toll-Like Receptor-Responsive Kinase, Protein Kinase R, Is Inactivated in Endotoxin Tolerance through Differential K63/K48 Ubiquitination.
|
| |
MBio,
1,
0.
|
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|
|
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|
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D.Moreno,
M.C.Towler,
D.G.Hardie,
E.Knecht,
and
P.Sanz
(2010).
The laforin-malin complex, involved in Lafora disease, promotes the incorporation of K63-linked ubiquitin chains into AMP-activated protein kinase beta subunits.
|
| |
Mol Biol Cell,
21,
2578-2588.
|
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|
|
|
|
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E.R.Weiss,
E.Popova,
H.Yamanaka,
H.C.Kim,
J.M.Huibregtse,
and
H.Göttlinger
(2010).
Rescue of HIV-1 release by targeting widely divergent NEDD4-type ubiquitin ligases and isolated catalytic HECT domains to Gag.
|
| |
PLoS Pathog,
6,
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|
|
|
|
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|
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F.Ikeda,
N.Crosetto,
and
I.Dikic
(2010).
What determines the specificity and outcomes of ubiquitin signaling?
|
| |
Cell,
143,
677-681.
|
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|
|
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|
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H.Fu,
Y.L.Lin,
and
A.S.Fatimababy
(2010).
Proteasomal recognition of ubiquitylated substrates.
|
| |
Trends Plant Sci,
15,
375-386.
|
|
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|
|
|
|
H.Habelhah
(2010).
Emerging complexity of protein ubiquitination in the NF-κB pathway.
|
| |
Genes Cancer,
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H.Kawabe,
A.Neeb,
K.Dimova,
S.M.Young,
M.Takeda,
S.Katsurabayashi,
M.Mitkovski,
O.A.Malakhova,
D.E.Zhang,
M.Umikawa,
K.Kariya,
S.Goebbels,
K.A.Nave,
C.Rosenmund,
O.Jahn,
J.Rhee,
and
N.Brose
(2010).
Regulation of Rap2A by the ubiquitin ligase Nedd4-1 controls neurite development.
|
| |
Neuron,
65,
358-372.
|
|
|
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|
|
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H.Su,
and
X.Wang
(2010).
The ubiquitin-proteasome system in cardiac proteinopathy: a quality control perspective.
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| |
Cardiovasc Res,
85,
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|
|
|
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|
|
|
H.Wu,
Y.C.Lo,
and
S.C.Lin
(2010).
Recent advances in polyubiquitin chain recognition.
|
| |
F1000 Biol Rep,
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|
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|
|
|
|
I.Bosanac,
I.E.Wertz,
B.Pan,
C.Yu,
S.Kusam,
C.Lam,
L.Phu,
Q.Phung,
B.Maurer,
D.Arnott,
D.S.Kirkpatrick,
V.M.Dixit,
and
S.G.Hymowitz
(2010).
Ubiquitin binding to A20 ZnF4 is required for modulation of NF-κB signaling.
|
| |
Mol Cell,
40,
548-557.
|
|
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PDB codes:
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|
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|
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I.E.Wertz,
and
V.M.Dixit
(2010).
Signaling to NF-kappaB: regulation by ubiquitination.
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| |
Cold Spring Harb Perspect Biol,
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J.Gautheron,
and
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(2010).
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Cell Mol Life Sci,
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T.Goncharov,
E.C.Dueber,
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K.Deshayes,
D.S.Kirkpatrick,
and
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(2010).
c-IAP1 and UbcH5 promote K11-linked polyubiquitination of RIP1 in TNF signalling.
|
| |
EMBO J,
29,
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and
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(2010).
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J Virol,
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and
V.M.Dixit
(2010).
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|
| |
Nature,
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N.M.Shanbhag,
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and
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Cell,
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|
| |
Mol Cell,
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only a partial list as not all journals are covered by
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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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