1cl4: 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:1cl4.png|left|200px]]
-<!--
+==NUCLEOCAPSID PROTEIN FROM MASON-PFIZER MONKEY VIRUS (MPMV)==
-The line below this paragraph, containing "STRUCTURE_1cl4", creates the "Structure Box" on the page.
+<StructureSection load='1cl4' size='340' side='right'caption='[[1cl4]]' 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'>[[1cl4]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mason-Pfizer_monkey_virus Mason-Pfizer monkey virus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CL4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1CL4 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">Solution NMR</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-{{STRUCTURE_1cl4|  PDB=1cl4  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1cl4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1cl4 OCA], [https://pdbe.org/1cl4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1cl4 RCSB], [https://www.ebi.ac.uk/pdbsum/1cl4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1cl4 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/GAG_MPMV GAG_MPMV] p10 is the matrix protein.  P14 is the nucleocapsid protein.  p27 is the capsid protein.
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/cl/1cl4_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</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=1cl4 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Retroviral nucleocapsid proteins (NCPs) are CCHC-type zinc finger proteins that mediate virion RNA binding activities associated with retrovirus assembly and genomic RNA encapsidation. Mason-Pfizer monkey virus (MPMV), a type D retrovirus, encodes a 96-amino acid nucleocapsid protein, which contains two Cys-X2-Cys-X4-His-X4-Cys (CCHC) zinc fingers connected by an unusually long 15-amino acid linker. Homonuclear, two-dimensional sensitivity-enhanced 15N-1H, three-dimensional 15N-1H, and triple resonance NMR spectroscopy have been used to determine the solution structure and residue-specific backbone dynamics of the structured core domain of MPMV NCP containing residues 21-80. Structure calculations and spectral density mapping of N-H bond vector mobility reveal that MPMV NCP 21-80 is best described as two independently folded, rotationally uncorrelated globular domains connected by a seven-residue flexible linker consisting of residues 42-48. The N-terminal CCHC zinc finger domain (residues 24-37) appears to adopt a fold like that described previously for HIV-1 NCP; however, residues within this domain and the immediately adjacent linker region (residues 38-41) are characterized by extensive conformational averaging on the micros-ms time scale at 25 degrees C. In contrast to other NCPs, residues 49-77, which includes the C-terminal CCHC zinc-finger (residues 53-66), comprise a well-folded globular domain with the Val49-Pro-Gly-Leu52 sequence and C-terminal tail residues 67-77 characterized by amide proton exchange properties and 15N R1, R2, and (1H-15N) NOE values indistinguishable to residues in the core C-terminal finger. Twelve refined structural models of MPMV NCP residues 49-80 (pairwise backbone RMSD of 0.77 A) reveal that the side chains of the conserved Pro50 and Trp62 are in van der Waals contact with one another. Residues 70-73 in the C-terminal tail adopt a reverse turn-like structure. Ile77 is involved in extensive van der Waals contact with the core finger domain, while the side chains of Ser68 and Asn75 appear to form hydrogen bonds that stabilize the overall fold of this domain. These residues outside of the core finger structure are conserved in D-type and related retroviral NCPs, e.g., MMTV NCP, suggesting that the structure of MPMV NCP may be representative of this subclass of retroviral NCPs.
-===NUCLEOCAPSID PROTEIN FROM MASON-PFIZER MONKEY VIRUS (MPMV)===
+Solution structure and backbone dynamics of Mason-Pfizer monkey virus (MPMV) nucleocapsid protein.,Gao Y, Kaluarachchi K, Giedroc DP Protein Sci. 1998 Nov;7(11):2265-80. PMID:9827993<ref>PMID:9827993</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1cl4" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_9827993}}, adds the Publication Abstract to the page
+*[[Gag polyprotein 3D structures|Gag polyprotein 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 9827993 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_9827993}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-CL4 is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Simian_mason-pfizer_virus Simian mason-pfizer virus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CL4 OCA].
+[[Category: Mason-Pfizer monkey virus]]
+[[Category: Gao Y]]
-==Reference==
+[[Category: Giedroc DP]]
-<ref group="xtra">PMID:9827993</ref><references group="xtra"/>
+[[Category: Kaluarachchi K]]
-[[Category: Simian mason-pfizer virus]]
-[[Category: Gao, Y.]]
-[[Category: Giedroc, D P.]]
-[[Category: Kaluarachchi, K.]]
-[[Category: Nucleocapsid protein]]
-[[Category: Retrovirus]]
-[[Category: Rna binding protein]]
-[[Category: Viral protein]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 13:22:09 2009''