2xi1: Difference between revisions

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-[[Image:2xi1.jpg|left|200px]]
-<!--
+==Crystal structure of the HIV-1 Nef sequenced from a patient's sample==
-The line below this paragraph, containing "STRUCTURE_2xi1", creates the "Structure Box" on the page.
+<StructureSection load='2xi1' size='340' side='right'caption='[[2xi1]], [[Resolution|resolution]] 3.50&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[2xi1]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Human_immunodeficiency_virus_type_1_(BH5_ISOLATE) Human immunodeficiency virus type 1 (BH5 ISOLATE)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XI1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2XI1 FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.5&#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=2xi1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xi1 OCA], [https://pdbe.org/2xi1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2xi1 RCSB], [https://www.ebi.ac.uk/pdbsum/2xi1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2xi1 ProSAT]</span></td></tr>
-{{STRUCTURE_2xi1|  PDB=2xi1  |  SCENE=  }}
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/C6KEI3_9HIV1 C6KEI3_9HIV1]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+HIV-1 Nef modulates disease progression through interactions with over 30 host proteins. Individual chains fold into membrane-interacting N-terminal and C-terminal core (Nef(core)) domains respectively. Nef exists as small oligomers near membranes and associates into higher oligomers such as tetramers or hexadecamers in the cytoplasm. Earlier structures of the Nef(core) in apo and complexed forms with the Fyn-kinase SH3 domain revealed dimeric association details and the role of the conserved PXXP recognition motif (residues 72-78) of Nef in SH3-domain interactions. The crystal structure of the tetrameric Nef reported here corresponds to the elusive cytoplasmic stage. Comparative analyses show that subunits of Nef(core) dimers (open conformation) swing out with a relative displacement of approximately 22 A and rotation of approximately 174 degrees to form the 'closed' tetrameric structure. The changes to the association are around Asp125, a conserved residue important for viral replication and the important XR motif (residues 107-108). The tetramer associates through C4 symmetry instead of the 222 symmetry expected when two dimers associate together. This novel dimer-tetramer transition agrees with earlier solution studies including small angle X-ray scattering, analytical ultracentrifugation, dynamic laser light scattering and our glutaraldehyde cross-linking experiments. Comparisons with the Nef(core)-Fyn-SH3 domain complexes reveal that the PXXP motif that interacts with the SH3-domain in the dimeric form is sterically occluded in the tetramer. However the 151-180 loop that is distal to the PXXP motif and contains several protein interaction motifs remains accessible. The results suggest how changes to the oligomeric state of Nef can help it distinguish between protein partners.
-===CRYSTAL STRUCTURE OF THE HIV-1 NEF SEQUENCED FROM A PATIENT'S SAMPLE===
+A Novel Dimer-Tetramer Transition Captured by the Crystal Structure of the HIV-1 Nef.,Singh P, Yadav GP, Gupta S, Tripathi AK, Ramachandran R, Tripathi RK PLoS One. 2011;6(11):e26629. Epub 2011 Nov 2. PMID:22073177<ref>PMID:22073177</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2xi1" style="background-color:#fffaf0;"></div>
-==About this Structure==
+==See Also==
-[[2xi1]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Viruses Viruses]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XI1 OCA].
+*[[Protein Nef 3D structures|Protein Nef 3D structures]]
-[[Category: Viruses]]
+== References ==
-[[Category: Gupta, S.]]
+<references/>
-[[Category: Ramachandran, R.]]
+__TOC__
-[[Category: Singh, P.]]
+</StructureSection>
-[[Category: Tripathi, A K.]]
+[[Category: Large Structures]]
-[[Category: Tripathi, R K.]]
+[[Category: Gupta S]]
-[[Category: Yadav, G P.]]
+[[Category: Ramachandran R]]
-[[Category: Aid]]
+[[Category: Singh P]]
-[[Category: Viral protein]]
+[[Category: Tripathi AK]]
+[[Category: Tripathi RK]]
+[[Category: Yadav GP]]