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PDBsum entry 3bia
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Immune system
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PDB id
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3bia
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Contents |
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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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Tim-4 in complex with sodium potassium tartrate
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Structure:
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T-cell immunoglobulin and mucin domain-containing protein 4. Chain: x. Fragment: n-terminal cys-rich domain. Synonym: timd-4, t-cell membrane protein 4, tim-4, spleen, mucin- containing, knockout of lymphotoxin protein, smuckler. Engineered: yes
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Source:
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Mus musculus. House mouse. Organism_taxid: 10090. Strain: knowles solter, c57bl/6j. Gene: timd4, tim4. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.
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Resolution:
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2.20Å
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R-factor:
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0.219
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R-free:
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0.238
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Authors:
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C.Santiago,A.Ballesteros,G.G.Kaplan,G.J.Freeman,J.M.Casasnovas
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Key ref:
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C.Santiago
et al.
(2007).
Structures of T cell immunoglobulin mucin protein 4 show a metal-Ion-dependent ligand binding site where phosphatidylserine binds.
Immunity,
27,
941-951.
PubMed id:
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Date:
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30-Nov-07
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Release date:
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01-Jan-08
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PROCHECK
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Headers
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References
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Q6U7R4
(TIMD4_MOUSE) -
T-cell immunoglobulin and mucin domain-containing protein 4 from Mus musculus
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Seq:
Struc:
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343 a.a.
110 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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Immunity
27:941-951
(2007)
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PubMed id:
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Structures of T cell immunoglobulin mucin protein 4 show a metal-Ion-dependent ligand binding site where phosphatidylserine binds.
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C.Santiago,
A.Ballesteros,
L.Martínez-Muñoz,
M.Mellado,
G.G.Kaplan,
G.J.Freeman,
J.M.Casasnovas.
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ABSTRACT
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The T cell immunoglobulin and mucin domain (TIM) proteins are important
regulators of T cell responses. Crystal structures of the murine TIM-4
identified a metal-ion-dependent ligand binding site (MILIBS) in the
immunoglobulin (Ig) domain of the TIM family. The characteristic CC' loop of the
TIM domain and the hydrophobic FG loop shaped a narrow cavity where acidic
compounds penetrate and coordinate to a metal ion bound to conserved residues in
the TIM proteins. The structure of phosphatidylserine bound to the Ig domain
showed that the hydrophilic head penetrates into the MILIBS and coordinates with
the metal ion, whereas the aromatic residues on the tip of the FG loop
interacted with the fatty acid chains and could insert into the lipid bilayer.
Our results also revealed an important role of the MILIBS in the trafficking of
TIM-1 to the cell surface.
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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.Y.Kim,
M.B.Eyheramonho,
M.Pichavant,
C.Gonzalez Cambaceres,
P.Matangkasombut,
G.Cervio,
S.Kuperman,
R.Moreiro,
K.Konduru,
M.Manangeeswaran,
G.J.Freeman,
G.G.Kaplan,
R.H.Dekruyff,
D.T.Umetsu,
and
S.D.Rosenzweig
(2011).
A polymorphism in TIM1 is associated with susceptibility to severe hepatitis A virus infection in humans.
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J Clin Invest,
121,
1111-1118.
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Y.Nakanishi,
K.Nagaosa,
and
A.Shiratsuchi
(2011).
Phagocytic removal of cells that have become unwanted: Implications for animal development and tissue homeostasis.
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Dev Growth Differ,
53,
149-160.
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C.D.Gregory,
and
J.D.Pound
(2010).
Microenvironmental influences of apoptosis in vivo and in vitro.
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Apoptosis,
15,
1029-1049.
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D.T.Umetsu,
and
R.H.Dekruyff
(2010).
99th Dahlem conference on infection, inflammation and chronic inflammatory disorders: microbes, apoptosis and TIM-1 in the development of asthma.
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Clin Exp Immunol,
160,
125-129.
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G.J.Freeman,
J.M.Casasnovas,
D.T.Umetsu,
and
R.H.DeKruyff
(2010).
TIM genes: a family of cell surface phosphatidylserine receptors that regulate innate and adaptive immunity.
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Immunol Rev,
235,
172-189.
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K.S.Ravichandran
(2010).
Find-me and eat-me signals in apoptotic cell clearance: progress and conundrums.
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J Exp Med,
207,
1807-1817.
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K.Wong,
P.A.Valdez,
C.Tan,
S.Yeh,
J.A.Hongo,
and
W.Ouyang
(2010).
Phosphatidylserine receptor Tim-4 is essential for the maintenance of the homeostatic state of resident peritoneal macrophages.
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Proc Natl Acad Sci U S A,
107,
8712-8717.
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L.P.Kane
(2010).
T cell Ig and mucin domain proteins and immunity.
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J Immunol,
184,
2743-2749.
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R.Rodriguez-Manzanet,
M.A.Sanjuan,
H.Y.Wu,
F.J.Quintana,
S.Xiao,
A.C.Anderson,
H.L.Weiner,
D.R.Green,
and
V.K.Kuchroo
(2010).
T and B cell hyperactivity and autoimmunity associated with niche-specific defects in apoptotic body clearance in TIM-4-deficient mice.
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Proc Natl Acad Sci U S A,
107,
8706-8711.
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S.S.Sonar,
Y.M.Hsu,
M.L.Conrad,
G.R.Majeau,
A.Kilic,
E.Garber,
Y.Gao,
C.Nwankwo,
G.Willer,
J.C.Dudda,
H.Kim,
V.Bailly,
A.Pagenstecher,
P.D.Rennert,
and
H.Renz
(2010).
Antagonism of TIM-1 blocks the development of disease in a humanized mouse model of allergic asthma.
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J Clin Invest,
120,
2767-2781.
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Y.Yamanishi,
J.Kitaura,
K.Izawa,
A.Kaitani,
Y.Komeno,
M.Nakamura,
S.Yamazaki,
Y.Enomoto,
T.Oki,
H.Akiba,
T.Abe,
T.Komori,
Y.Morikawa,
H.Kiyonari,
T.Takai,
K.Okumura,
and
T.Kitamura
(2010).
TIM1 is an endogenous ligand for LMIR5/CD300b: LMIR5 deficiency ameliorates mouse kidney ischemia/reperfusion injury.
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J Exp Med,
207,
1501-1511.
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C.D.Gregory,
J.D.Pound,
A.Devitt,
M.Wilson-Jones,
P.Ray,
and
R.J.Murray
(2009).
Inhibitory effects of persistent apoptotic cells on monoclonal antibody production in vitro: simple removal of non-viable cells improves antibody productivity by hybridoma cells in culture.
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MAbs,
1,
370-376.
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H.Hemmi,
J.Idoyaga,
K.Suda,
N.Suda,
K.Kennedy,
M.Noda,
A.Aderem,
and
R.M.Steinman
(2009).
A new triggering receptor expressed on myeloid cells (Trem) family member, Trem-like 4, binds to dead cells and is a DNAX activation protein 12-linked marker for subsets of mouse macrophages and dendritic cells.
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J Immunol,
182,
1278-1286.
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K.Chattopadhyay,
E.Lazar-Molnar,
Q.Yan,
R.Rubinstein,
C.Zhan,
V.Vigdorovich,
U.A.Ramagopal,
J.Bonanno,
S.G.Nathenson,
and
S.C.Almo
(2009).
Sequence, structure, function, immunity: structural genomics of costimulation.
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Immunol Rev,
229,
356-386.
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L.Walter,
and
H.Neumann
(2009).
Role of microglia in neuronal degeneration and regeneration.
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Semin Immunopathol,
31,
513-525.
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M.Nakayama,
H.Akiba,
K.Takeda,
Y.Kojima,
M.Hashiguchi,
M.Azuma,
H.Yagita,
and
K.Okumura
(2009).
Tim-3 mediates phagocytosis of apoptotic cells and cross-presentation.
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Blood,
113,
3821-3830.
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R.Rodriguez-Manzanet,
R.DeKruyff,
V.K.Kuchroo,
and
D.T.Umetsu
(2009).
The costimulatory role of TIM molecules.
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Immunol Rev,
229,
259-270.
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A.J.de Souza,
J.S.Oak,
R.Jordanhazy,
R.H.DeKruyff,
D.A.Fruman,
and
L.P.Kane
(2008).
T cell Ig and mucin domain-1-mediated T cell activation requires recruitment and activation of phosphoinositide 3-kinase.
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J Immunol,
180,
6518-6526.
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D.A.Hafler,
and
V.Kuchroo
(2008).
TIMs: central regulators of immune responses.
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J Exp Med,
205,
2699-2701.
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E.W.Su,
J.Y.Lin,
and
L.P.Kane
(2008).
TIM-1 and TIM-3 proteins in immune regulation.
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Cytokine,
44,
9.
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G.Acosta-Pérez,
M.Maximina Bertha Moreno-Altamirano,
G.Rodríguez-Luna,
and
F.Javier Sánchez-Garcia
(2008).
Differential dependence of the ingestion of necrotic cells and TNF-alpha / IL-1beta production by murine macrophages on lipid rafts.
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Scand J Immunol,
68,
423-429.
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T.Ichimura,
E.J.Asseldonk,
B.D.Humphreys,
L.Gunaratnam,
J.S.Duffield,
and
J.V.Bonventre
(2008).
Kidney injury molecule-1 is a phosphatidylserine receptor that confers a phagocytic phenotype on epithelial cells.
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J Clin Invest,
118,
1657-1668.
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V.K.Kuchroo,
V.Dardalhon,
S.Xiao,
and
A.C.Anderson
(2008).
New roles for TIM family members in immune regulation.
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Nat Rev Immunol,
8,
577-580.
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Y.Q.Xiao,
C.G.Freire-de-Lima,
W.P.Schiemann,
D.L.Bratton,
R.W.Vandivier,
and
P.M.Henson
(2008).
Transcriptional and translational regulation of TGF-beta production in response to apoptotic cells.
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J Immunol,
181,
3575-3585.
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J.Savill,
and
C.Gregory
(2007).
Apoptotic PS to phagocyte TIM-4: eat me.
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Immunity,
27,
830-832.
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N.Kobayashi,
P.Karisola,
V.Peña-Cruz,
D.M.Dorfman,
M.Jinushi,
S.E.Umetsu,
M.J.Butte,
H.Nagumo,
I.Chernova,
B.Zhu,
A.H.Sharpe,
S.Ito,
G.Dranoff,
G.G.Kaplan,
J.M.Casasnovas,
D.T.Umetsu,
R.H.Dekruyff,
and
G.J.Freeman
(2007).
TIM-1 and TIM-4 glycoproteins bind phosphatidylserine and mediate uptake of apoptotic cells.
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Immunity,
27,
927-940.
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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.
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Links
