3ik5: Difference between revisions

From Proteopedia
Jump to navigationJump to search
← Older edit
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,328,572 edits
No edit summary
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,328,572 edits
No edit summary
 
Line 3: Line 3:
<StructureSection load='3ik5' size='340' side='right'caption='[[3ik5]], [[Resolution|resolution]] 2.05&Aring;' scene=''>
<StructureSection load='3ik5' size='340' side='right'caption='[[3ik5]], [[Resolution|resolution]] 2.05&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3ik5]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Siv_-_cpz Siv - cpz]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IK5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IK5 FirstGlance]. <br>
<table><tr><td colspan='2'>[[3ik5]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Simian_immunodeficiency_virus_-_cpz Simian immunodeficiency virus - cpz]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IK5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IK5 FirstGlance]. <br>
</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">nef ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=388909 SIV - cpz])</td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.05&#8491;</td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3ik5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ik5 OCA], [https://pdbe.org/3ik5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ik5 RCSB], [https://www.ebi.ac.uk/pdbsum/3ik5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ik5 ProSAT]</span></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3ik5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ik5 OCA], [https://pdbe.org/3ik5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ik5 RCSB], [https://www.ebi.ac.uk/pdbsum/3ik5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ik5 ProSAT]</span></td></tr>
</table>
</table>
== Disease ==
[[https://www.uniprot.org/uniprot/CD3Z_HUMAN CD3Z_HUMAN]] Defects in CD247 are the cause of immunodeficiency due to defect in CD3-zeta (CD3ZID) [MIM:[https://omim.org/entry/610163 610163]]. An immunological deficiency characterized by T-cells impaired immune response to alloantigens, tetanus toxoid and mitogens.<ref>PMID:16672702</ref> 
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/CD3Z_HUMAN CD3Z_HUMAN]] Probable role in assembly and expression of the TCR complex as well as signal transduction upon antigen triggering.  
[https://www.uniprot.org/uniprot/NEF_SIVMA NEF_SIVMA] Seems to play a role in optimizing the host cell environment for viral replication without causing cell death by apoptosis. Enhances virus infectivity and pathogenicity. Probably involved in viral immune evasion mechanisms (By similarity).  In infected CD4(+) T-lymphocytes, down-regulates cell surface expression of CD4, CD28, CD3, and MHC-I or MHC-II molecules.  Interferes with TCR signaling from the cell membrane. Interacts with CD247/TCRZ (TCR zeta chain) and exert potent down-regulation of cell surface TCR/CD3 complexes (By similarity).
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
Line 21: Line 19:
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3ik5 ConSurf].
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3ik5 ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
HIV/SIV Nef mediates many cellular processes through interactions with various cytoplasmic and membrane-associated host proteins, including the signalling zeta subunit of the T-cell receptor (TCRzeta). Here, the crystallization strategy, methods and refinement procedures used to solve the structures of the core domain of the SIVmac239 isolate of Nef (Nef(core)) in complex with two different TCRzeta fragments are described. The structure of SIVmac239 Nef(core) bound to the longer TCRzeta polypeptide (Leu51-Asp93) was determined to 3.7 A resolution (R(work) = 28.7%) in the tetragonal space group P4(3)2(1)2. The structure of SIVmac239 Nef(core) in complex with the shorter TCRzeta polypeptide (Ala63-Arg80) was determined to 2.05 A resolution (R(work) = 17.0%), but only after the detection of nearly perfect pseudo-merohedral crystal twinning and proper assignment of the orthorhombic space group P2(1)2(1)2(1). The reduction in crystal space-group symmetry induced by the truncated TCRzeta polypeptide appears to be caused by the rearrangement of crystal-contact hydrogen-bonding networks and the substitution of crystallographic symmetry operations by similar noncrystallographic symmetry (NCS) operations. The combination of NCS rotations that were nearly parallel to the twin operation (k, h, -l) and a and b unit-cell parameters that were nearly identical predisposed the P2(1)2(1)2(1) crystal form to pseudo-merohedral twinning.
Pseudo-merohedral twinning and noncrystallographic symmetry in orthorhombic crystals of SIVmac239 Nef core domain bound to different-length TCRzeta fragments.,Kim WM, Sigalov AB, Stern LJ Acta Crystallogr D Biol Crystallogr. 2010 Feb;66(Pt 2):163-75. Epub 2010 Jan 22. PMID:20124696<ref>PMID:20124696</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3ik5" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[CD3 3D structures|CD3 3D structures]]
*[[CD3 3D structures|CD3 3D structures]]
*[[Protein Nef|Protein Nef]]
*[[Protein Nef 3D structures|Protein Nef 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Homo sapiens]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Siv - cpz]]
[[Category: Simian immunodeficiency virus - cpz]]
[[Category: Kim, W M]]
[[Category: Kim WM]]
[[Category: Sigalov, A B]]
[[Category: Sigalov AB]]
[[Category: Stern, L J]]
[[Category: Stern LJ]]
[[Category: Cell membrane]]
[[Category: Disulfide bond]]
[[Category: Host-virus interaction]]
[[Category: Lipoprotein]]
[[Category: Membrane]]
[[Category: Myristate]]
[[Category: Phosphoprotein]]
[[Category: Protein-protein complex]]
[[Category: Receptor]]
[[Category: Transmembrane]]
[[Category: Viral immunoevasion]]
[[Category: Viral protein-antiviral protein complex]]
[[Category: Viral protein-signaling protein complex]]
[[Category: Virulence]]
Retrieved from "https://proteopedia.org/3ik5"