3oe6: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-{{Seed}}
-[[Image:3oe6.jpg|left|200px]]
-<!--
+==Crystal structure of the CXCR4 chemokine receptor in complex with a small molecule antagonist IT1t in I222 spacegroup==
-The line below this paragraph, containing "STRUCTURE_3oe6", creates the "Structure Box" on the page.
+<StructureSection load='3oe6' size='340' side='right'caption='[[3oe6]], [[Resolution|resolution]] 3.20&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'>[[3oe6]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_virus_T4 Escherichia virus T4] and [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3OE6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3OE6 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]] 3.2&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=ITD:(6,6-DIMETHYL-5,6-DIHYDROIMIDAZO[2,1-B][1,3]THIAZOL-3-YL)METHYL+N,N-DICYCLOHEXYLIMIDOTHIOCARBAMATE'>ITD</scene>, <scene name='pdbligand=OLC:(2R)-2,3-DIHYDROXYPROPYL+(9Z)-OCTADEC-9-ENOATE'>OLC</scene></td></tr>
-{{STRUCTURE_3oe6|  PDB=3oe6  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3oe6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3oe6 OCA], [https://pdbe.org/3oe6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3oe6 RCSB], [https://www.ebi.ac.uk/pdbsum/3oe6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3oe6 ProSAT]</span></td></tr>
+</table>
+== Disease ==
+[https://www.uniprot.org/uniprot/CXCR4_HUMAN CXCR4_HUMAN] Defects in CXCR4 are a cause of WHIM syndrome (WHIM) [MIM:[https://omim.org/entry/193670 193670]; also known as warts, hypogammaglobulinemia, infections and myelokathexis. WHIM syndrome is an immunodeficiency disease characterized by neutropenia, hypogammaglobulinemia and extensive human papillomavirus (HPV) infection. Despite the peripheral neutropenia, bone marrow aspirates from affected individuals contain abundant mature myeloid cells, a condition termed myelokathexis.<ref>PMID:12692554</ref>
+== Function ==
+[https://www.uniprot.org/uniprot/CXCR4_HUMAN CXCR4_HUMAN] Receptor for the C-X-C chemokine CXCL12/SDF-1 that transduces a signal by increasing intracellular calcium ion levels and enhancing MAPK1/MAPK3 activation. Acts as a receptor for extracellular ubiquitin; leading to enhanced intracellular calcium ions and reduced cellular cAMP levels. Involved in hematopoiesis and in cardiac ventricular septum formation. Also plays an essential role in vascularization of the gastrointestinal tract, probably by regulating vascular branching and/or remodeling processes in endothelial cells. Involved in cerebellar development. In the CNS, could mediate hippocampal-neuron survival. Acts as a coreceptor (CD4 being the primary receptor) for HIV-1 X4 isolates and as a primary receptor for some HIV-2 isolates. Promotes Env-mediated fusion of the virus.<ref>PMID:8329116</ref> <ref>PMID:8234909</ref> <ref>PMID:8629022</ref> <ref>PMID:8752280</ref> <ref>PMID:8752281</ref> <ref>PMID:10074102</ref> <ref>PMID:10644702</ref> <ref>PMID:10825158</ref> <ref>PMID:17197449</ref> <ref>PMID:20048153</ref> <ref>PMID:20228059</ref> <ref>PMID:20505072</ref> [https://www.uniprot.org/uniprot/ENLYS_BPT4 ENLYS_BPT4] Endolysin with lysozyme activity that degrades host peptidoglycans and participates with the holin and spanin proteins in the sequential events which lead to the programmed host cell lysis releasing the mature viral particles. Once the holin has permeabilized the host cell membrane, the endolysin can reach the periplasm and break down the peptidoglycan layer.<ref>PMID:22389108</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Chemokine receptors are critical regulators of cell migration in the context of immune surveillance, inflammation, and development. The G protein-coupled chemokine receptor, CXCR4, is specifically implicated in cancer metastasis and HIV-1 infection. Here, we report five independent crystal structures of CXCR4 bound to an antagonist small molecule IT1t and a cyclic peptide CVX15 at 2.5 to 3.2 angstrom resolution. All structures reveal a consistent homodimer with an interface including helices V and VI that may be involved in regulating signaling. The location and shape of the ligand-binding sites differ from other G protein-coupled receptors (GPCRs) and are closer to the extracellular surface. These structures provide new clues about the interactions between CXCR4 and its natural ligand CXCL12 and with the HIV-1 glycoprotein gp120.
-===Crystal structure of the CXCR4 chemokine receptor in complex with a small molecule antagonist IT1t in I222 spacegroup===
+Structures of the CXCR4 Chemokine GPCR with Small-Molecule and Cyclic Peptide Antagonists.,Wu B, Chien EY, Mol CD, Fenalti G, Liu W, Katritch V, Abagyan R, Brooun A, Wells P, Bi FC, Hamel DJ, Kuhn P, Handel TM, Cherezov V, Stevens RC Science. 2010 Oct 7. PMID:20929726<ref>PMID:20929726</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3oe6" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_20929726}}, adds the Publication Abstract to the page
+*[[CXC chemokine receptor|CXC chemokine receptor]]
-(as it appears on PubMed at http://www.pubmed.gov), where 20929726 is the PubMed ID number.
+*[[CXC chemokine receptor type 4|CXC chemokine receptor type 4]]
--->
+*[[Lysozyme 3D structures|Lysozyme 3D structures]]
-{{ABSTRACT_PUBMED_20929726}}
+== References ==
+<references/>
-==About this Structure==
+__TOC__
-OE6 is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapien,_enterobacteria_phage_t4 Homo sapien, enterobacteria phage t4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3OE6 OCA].
+</StructureSection>
+[[Category: Escherichia virus T4]]
-==Reference==
+[[Category: Homo sapiens]]
-<ref group="xtra">PMID:20929726</ref><references group="xtra"/>
+[[Category: Large Structures]]
-[[Category: Homo sapien, enterobacteria phage t4]]
+[[Category: Cherezov V]]
-[[Category: Lysozyme]]
+[[Category: Chien EYT]]
-[[Category: ATCG3D, Accelerated Technologies Center for Gene to 3D Structure.]]
+[[Category: Han GW]]
-[[Category: Cherezov, V.]]
+[[Category: Katritch V]]
-[[Category: Chien, E Y.T.]]
+[[Category: Liu W]]
-[[Category: Han, G W.]]
+[[Category: Mol CD]]
-[[Category: Katritch, V.]]
+[[Category: Stevens RC]]
-[[Category: Liu, W.]]
+[[Category: Wu B]]
-[[Category: Mol, C D.]]
-[[Category: Stevens, R C.]]
-[[Category: Wu, B.]]
-[[Category: 7tm]]
-[[Category: Accelerated technologies center for gene to 3d structure]]
-[[Category: Atcg3d]]
-[[Category: Cancer]]
-[[Category: Chemokine]]
-[[Category: Chimera]]
-[[Category: Cxcl12]]
-[[Category: G protein-coupled receptor]]
-[[Category: Gpcr]]
-[[Category: Hiv-1 co-receptor]]
-[[Category: Hydrolase]]
-[[Category: Isothiourea]]
-[[Category: It1t]]
-[[Category: Membrane protein]]
-[[Category: Protein structure initiative]]
-[[Category: Psi-2]]
-[[Category: Sdf1]]
-[[Category: Signal transduction]]
-[[Category: Singnaling protein]]
-[[Category: Structural genomic]]
-[[Category: T4l fusion]]
-[[Category: Transmembrane]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Oct 27 12:14:20 2010''