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PDBsum entry 2k4f

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Immune system, signaling protein PDB id
2k4f

 

 

 

 

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Contents
Protein chain
57 a.a. *
* Residue conservation analysis
PDB id:
2k4f
Name: Immune system, signaling protein
Title: Mouse cd3epsilon cytoplasmic tail
Structure: T-cell surface glycoprotein cd3 epsilon chain. Chain: a. Fragment: cytoplasmic domain. Synonym: t-cell surface antigen t3/leu-4 epsilon chain. Engineered: yes
Source: Mus musculus. Mouse. Organism_taxid: 10090. Gene: cd3e. Expressed in: escherichia coli.
NMR struc: 20 models
Authors: C.Xu,M.E.Call,C.D.Schwieters,J.R.Schnell,E.E.Gagnon, K.W.Wucherpfennig,J.J.Chou
Key ref:
C.Xu et al. (2008). Regulation of T cell receptor activation by dynamic membrane binding of the CD3epsilon cytoplasmic tyrosine-based motif. Cell, 135, 702-713. PubMed id: 19013279 DOI: 10.1016/j.cell.2008.09.044
Date:
07-Jun-08     Release date:   02-Dec-08    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P22646  (CD3E_MOUSE) -  T-cell surface glycoprotein CD3 epsilon chain from Mus musculus
Seq:
Struc:
189 a.a.
57 a.a.*
Key:    PfamA domain  Secondary structure
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.?
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

 

 
DOI no: 10.1016/j.cell.2008.09.044 Cell 135:702-713 (2008)
PubMed id: 19013279  
 
 
Regulation of T cell receptor activation by dynamic membrane binding of the CD3epsilon cytoplasmic tyrosine-based motif.
C.Xu, E.Gagnon, M.E.Call, J.R.Schnell, C.D.Schwieters, C.V.Carman, J.J.Chou, K.W.Wucherpfennig.
 
  ABSTRACT  
 
Many immune system receptors signal through cytoplasmic tyrosine-based motifs (ITAMs), but how receptor ligation results in ITAM phosphorylation remains unknown. Live-cell imaging studies showed a close interaction of the CD3epsilon cytoplasmic domain of the T cell receptor (TCR) with the plasma membrane through fluorescence resonance energy transfer between a C-terminal fluorescent protein and a membrane fluorophore. Electrostatic interactions between basic CD3epsilon residues and acidic phospholipids enriched in the inner leaflet of the plasma membrane were required for binding. The nuclear magnetic resonance structure of the lipid-bound state of this cytoplasmic domain revealed deep insertion of the two key tyrosines into the hydrophobic core of the lipid bilayer. Receptor ligation thus needs to result in unbinding of the CD3epsilon ITAM from the membrane to render these tyrosines accessible to Src kinases. Sequestration of key tyrosines into the lipid bilayer represents a previously unrecognized mechanism for control of receptor activation.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. The CD3 epsilon Cytoplasmic Domain Is Bound to the Inner Leaflet of the Plasma Membrane
(A and C) The FRET efficiency was determined for transfectants expressing the CD3 epsilon WT or a CD3 epsilon mutant cytoplasmic domain (Emut1+2) (10 cells/construct, error bars indicate SEM) using the quenching approach, as in Figures 2C and 2E. R18-PB: R18 photobleached.
(B and D) The donor dequenching method was used to measure the FRET efficiency for the same transfectants (20 cells shown here from one experiment), as in Figures 2D and 2F.
Figure 7.
Figure 7. Membrane Binding Renders the Tyrosines of CD3 epsilon Inaccessible to Lck
(A) Lipid binding prevents tyrosine phosphorylation of CD3 epsilon [CD]. The tyrosine residues of CD3 epsilon [CD] were efficiently phosphorylated by Lck in an in vitro kinase assay. Addition of POPG/DHPC bicelles but not control POPC/DHPC bicelles prevented tyrosine phosphorylation. Western blots were probed with a phospho-tyrosine antibody (biotinylated P-Tyr-100 and streptavidin-horseradish peroxidase, SA-HRP) and a CD3 epsilon [CD] antibody (CD3 epsilon m20 and anti-goat IgG-HRP).
(B) Neither endogenous CD3 epsilon nor the HA-KIR-CD3 epsilon [CD]-TFP reporter protein are basally phosphorylated. HA-KIR-CD3 epsilon [CD]-TFP transfected Jurkat cells were solubilized using 1% NP40 and proteins were immunoprecipitated with CD3ζ (6B10.2), CD3 epsilon (UCHT1), HA (3F10), or FLAG (M2, isotype control) antibodies. Phosphorylated and total proteins were detected with a phospho-tyrosine antibody (biotinylated P-Tyr-100 and SA-HRP, upper panel), a CD3 epsilon [CD] antibody (CD3 epsilon m20 and anti-goat IgG-HRP, which detects CD3 epsilon and the reporter protein), or an antibody to the ζ chain (anti-CD3ζ 6B10.2-HRP, lower panel). SDS-PAGE was performed under nonreducing conditions.
 
  The above figures are reprinted from an Open Access publication published by Cell Press: Cell (2008, 135, 702-713) copyright 2008.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
23201688 X.Shi, Y.Bi, W.Yang, X.Guo, Y.Jiang, C.Wan, L.Li, Y.Bai, J.Guo, Y.Wang, X.Chen, B.Wu, H.Sun, W.Liu, J.Wang, and C.Xu (2013).
Ca2+ regulates T-cell receptor activation by modulating the charge property of lipids.
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22763440 J.R.James, and R.D.Vale (2012).
Biophysical mechanism of T-cell receptor triggering in a reconstituted system.
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21179118 L.Balagopalan, E.Sherman, V.A.Barr, and L.E.Samelson (2011).
Imaging techniques for assaying lymphocyte activation in action.
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21904389 M.L.Dustin, and D.Depoil (2011).
New insights into the T cell synapse from single molecule techniques.
  Nat Rev Immunol, 11, 672-684.  
21423173 M.Yabas, C.E.Teh, S.Frankenreiter, D.Lal, C.M.Roots, B.Whittle, D.T.Andrews, Y.Zhang, N.C.Teoh, J.Sprent, L.E.Tze, E.M.Kucharska, J.Kofler, G.C.Farell, S.Bröer, C.C.Goodnow, and A.Enders (2011).
ATP11C is critical for the internalization of phosphatidylserine and differentiation of B lymphocytes.
  Nat Immunol, 12, 441-449.  
21256056 N.Jiang, J.Huang, L.J.Edwards, B.Liu, Y.Zhang, C.D.Beal, B.D.Evavold, and C.Zhu (2011).
Two-stage cooperative T cell receptor-peptide major histocompatibility complex-CD8 trimolecular interactions amplify antigen discrimination.
  Immunity, 34, 13-23.  
21127503 P.A.van der Merwe, and O.Dushek (2011).
Mechanisms for T cell receptor triggering.
  Nat Rev Immunol, 11, 47-55.  
21190897 S.J.Davis, and P.A.van der Merwe (2011).
Lck and the nature of the T cell receptor trigger.
  Trends Immunol, 32, 1-5.  
20174674 A.B.Sigalov (2010).
Protein intrinsic disorder and oligomericity in cell signaling.
  Mol Biosyst, 6, 451-461.  
  21487502 A.B.Sigalov (2010).
Unusual biophysics of immune signaling-related intrinsically disordered proteins.
  Self Nonself, 1, 271-281.  
  21487511 A.B.Sigalov (2010).
The SCHOOL of nature: II. Protein order, disorder and oligomericity in transmembrane signaling.
  Self Nonself, 1, 89.  
  21487515 A.B.Sigalov (2010).
Membrane binding of intrinsically disordered proteins: Critical importance of an appropriate membrane model.
  Self Nonself, 1, 129-132.  
20029448 A.K.Chakraborty, and J.Das (2010).
Pairing computation with experimentation: a powerful coupling for understanding T cell signalling.
  Nat Rev Immunol, 10, 59-71.  
20010844 B.F.Lillemeier, M.A.Mörtelmaier, M.B.Forstner, J.B.Huppa, J.T.Groves, and M.M.Davis (2010).
TCR and Lat are expressed on separate protein islands on T cell membranes and concatenate during activation.
  Nat Immunol, 11, 90-96.  
20171124 B.Treanor, D.Depoil, A.Gonzalez-Granja, P.Barral, M.Weber, O.Dushek, A.Bruckbauer, and F.D.Batista (2010).
The membrane skeleton controls diffusion dynamics and signaling through the B cell receptor.
  Immunity, 32, 187-199.  
20434893 B.Treanor, and F.D.Batista (2010).
Organisation and dynamics of antigen receptors: implications for lymphocyte signalling.
  Curr Opin Immunol, 22, 299-307.  
21156831 D.G.Metcalf, D.T.Moore, Y.Wu, J.M.Kielec, K.Molnar, K.G.Valentine, A.J.Wand, J.S.Bennett, and W.F.DeGrado (2010).
NMR analysis of the alphaIIb beta3 cytoplasmic interaction suggests a mechanism for integrin regulation.
  Proc Natl Acad Sci U S A, 107, 22481-22486.
PDB code: 2kv9
20439542 D.R.Fooksman, and M.L.Dustin (2010).
Affinity measured by microcluster.
  J Exp Med, 207, 907-909.  
19968559 D.R.Fooksman, S.Vardhana, G.Vasiliver-Shamis, J.Liese, D.A.Blair, J.Waite, C.Sacristán, G.D.Victora, A.Zanin-Zhorov, and M.L.Dustin (2010).
Functional anatomy of T cell activation and synapse formation.
  Annu Rev Immunol, 28, 79.  
20813252 E.Gagnon, C.Xu, W.Yang, H.H.Chu, M.E.Call, J.J.Chou, and K.W.Wucherpfennig (2010).
Response multilayered control of T cell receptor phosphorylation.
  Cell, 142, 669-671.  
20727037 F.D.Batista, B.Treanor, and N.E.Harwood (2010).
Visualizing a role for the actin cytoskeleton in the regulation of B-cell activation.
  Immunol Rev, 237, 191-204.  
20150895 H.Wang, J.Holst, S.R.Woo, C.Guy, M.Bettini, Y.Wang, A.Shafer, M.Naramura, M.Mingueneau, L.L.Dragone, S.M.Hayes, B.Malissen, H.Band, and D.A.Vignali (2010).
Tonic ubiquitylation controls T-cell receptor:CD3 complex expression during T-cell development.
  EMBO J, 29, 1285-1298.  
20541955 K.Nika, C.Soldani, M.Salek, W.Paster, A.Gray, R.Etzensperger, L.Fugger, P.Polzella, V.Cerundolo, O.Dushek, T.Höfer, A.Viola, and O.Acuto (2010).
Constitutively active Lck kinase in T cells drives antigen receptor signal transduction.
  Immunity, 32, 766-777.  
  20452950 K.W.Wucherpfennig, E.Gagnon, M.J.Call, E.S.Huseby, and M.E.Call (2010).
Structural biology of the T-cell receptor: insights into receptor assembly, ligand recognition, and initiation of signaling.
  Cold Spring Harb Perspect Biol, 2, a005140.  
20849190 M.Artomov, M.Kardar, and A.K.Chakraborty (2010).
Only signaling modules that discriminate sharply between stimulatory and nonstimulatory inputs require basal signaling for fast cellular responses.
  J Chem Phys, 133, 105101.  
21134635 M.E.Call, and J.J.Chou (2010).
A view into the blind spot: solution NMR provides new insights into signal transduction across the lipid bilayer.
  Structure, 18, 1559-1569.  
20192804 N.E.Harwood, and F.D.Batista (2010).
Early events in B cell activation.
  Annu Rev Immunol, 28, 185-210.  
  20516133 P.E.Love, and S.M.Hayes (2010).
ITAM-mediated signaling by the T-cell antigen receptor.
  Cold Spring Harb Perspect Biol, 2, a002485.  
20813251 R.A.Fernandes, C.Yu, A.M.Carmo, E.J.Evans, P.A.van der Merwe, and S.J.Davis (2010).
What controls T cell receptor phosphorylation?
  Cell, 142, 668-669.  
21152094 S.Dong, B.Corre, K.Nika, S.Pellegrini, and F.Michel (2010).
T cell receptor signal initiation induced by low-grade stimulation requires the cooperation of LAT in human T cells.
  PLoS One, 5, e15114.  
20935671 S.K.Pierce, and W.Liu (2010).
The tipping points in the initiation of B cell signalling: how small changes make big differences.
  Nat Rev Immunol, 10, 767-777.  
19836999 Z.Ma, and T.H.Finkel (2010).
T cell receptor triggering by force.
  Trends Immunol, 31, 1-6.  
19940238 A.A.Schmaier, Z.Zou, A.Kazlauskas, L.Emert-Sedlak, K.P.Fong, K.B.Neeves, S.F.Maloney, S.L.Diamond, S.P.Kunapuli, J.Ware, L.F.Brass, T.E.Smithgall, K.Saksela, and M.L.Kahn (2009).
Molecular priming of Lyn by GPVI enables an immune receptor to adopt a hemostatic role.
  Proc Natl Acad Sci U S A, 106, 21167-21172.  
19733547 A.B.Sigalov, and G.M.Hendricks (2009).
Membrane binding mode of intrinsically disordered cytoplasmic domains of T cell receptor signaling subunits depends on lipid composition.
  Biochem Biophys Res Commun, 389, 388-393.  
19909352 C.S.Guy, and D.A.Vignali (2009).
Organization of proximal signal initiation at the TCR:CD3 complex.
  Immunol Rev, 232, 7.  
19132916 J.E.Smith-Garvin, G.A.Koretzky, and M.S.Jordan (2009).
T cell activation.
  Annu Rev Immunol, 27, 591-619.  
19819936 J.F.Brodeur, S.Li, O.Damlaj, and V.P.Dave (2009).
Expression of fully assembled TCR-CD3 complex on double positive thymocytes: synergistic role for the PRS and ER retention motifs in the intra-cytoplasmic tail of CD3epsilon.
  Int Immunol, 21, 1317-1327.  
19898475 J.Wang, R.M.Pielak, M.A.McClintock, and J.J.Chou (2009).
Solution structure and functional analysis of the influenza B proton channel.
  Nat Struct Mol Biol, 16, 1267-1271.
PDB codes: 2kix 2kj1
19628870 K.Choudhuri, M.Parker, A.Milicic, D.K.Cole, M.K.Shaw, A.K.Sewell, G.Stewart-Jones, T.Dong, K.G.Gould, and P.A.van der Merwe (2009).
Peptide-major histocompatibility complex dimensions control proximal kinase-phosphatase balance during T cell activation.
  J Biol Chem, 284, 26096-26105.  
19646256 L.Kurgan, A.A.Razib, S.Aghakhani, S.Dick, M.Mizianty, and S.Jahandideh (2009).
CRYSTALP2: sequence-based protein crystallization propensity prediction.
  BMC Struct Biol, 9, 50.  
19542373 L.M.Deford-Watts, T.C.Tassin, A.M.Becker, J.J.Medeiros, J.P.Albanesi, P.E.Love, C.Wülfing, and N.S.van Oers (2009).
The cytoplasmic tail of the T cell receptor CD3 epsilon subunit contains a phospholipid-binding motif that regulates T cell functions.
  J Immunol, 183, 1055-1064.  
19371714 M.L.Dustin (2009).
The cellular context of T cell signaling.
  Immunity, 30, 482-492.  
19500675 M.L.Dustin (2009).
Supported bilayers at the vanguard of immune cell activation studies.
  J Struct Biol, 168, 152-160.  
19909354 P.Tolar, H.W.Sohn, W.Liu, and S.K.Pierce (2009).
The molecular assembly and organization of signaling active B-cell receptor oligomers.
  Immunol Rev, 232, 34-41.  
19282883 P.Tolar, and S.K.Pierce (2009).
Change we can believe in--of the conformational type. Workshop on the Initiation of Antigen Receptor Signaling.
  EMBO Rep, 10, 331-336.  
19625641 R.Wang, K.Natarajan, and D.H.Margulies (2009).
Structural basis of the CD8 alpha beta/MHC class I interaction: focused recognition orients CD8 beta to a T cell proximal position.
  J Immunol, 183, 2554-2564.
PDB codes: 3dmm 3ecb
19406478 T.E.Singleton, B.Platzer, E.Dehlink, and E.Fiebiger (2009).
The first transmembrane region of the beta-chain stabilizes the tetrameric Fc epsilon RI complex.
  Mol Immunol, 46, 2333-2339.  
19732448 T.Harder, and D.Sangani (2009).
Plasma membrane rafts engaged in T cell signalling: new developments in an old concept.
  Cell Commun Signal, 7, 21.  
19177148 T.Zech, C.S.Ejsing, K.Gaus, B.de Wet, A.Shevchenko, K.Simons, and T.Harder (2009).
Accumulation of raft lipids in T-cell plasma membrane domains engaged in TCR signalling.
  EMBO J, 28, 466-476.  
19909353 V.P.Dave (2009).
Hierarchical role of CD3 chains in thymocyte development.
  Immunol Rev, 232, 22-33.  
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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