1r7r: Difference between revisions

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-{{Seed}}
-[[Image:1r7r.png|left|200px]]
-<!--
+==The crystal structure of murine p97/VCP at 3.6A==
-The line below this paragraph, containing "STRUCTURE_1r7r", creates the "Structure Box" on the page.
+<StructureSection load='1r7r' size='340' side='right'caption='[[1r7r]], [[Resolution|resolution]] 3.60&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'>[[1r7r]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. The August 2006 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''AAA+ Proteases''  by David S. Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2006_8 10.2210/rcsb_pdb/mom_2006_8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1R7R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1R7R 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]] 3.6&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene></td></tr>
-{{STRUCTURE_1r7r|  PDB=1r7r  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1r7r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1r7r OCA], [https://pdbe.org/1r7r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1r7r RCSB], [https://www.ebi.ac.uk/pdbsum/1r7r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1r7r ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/TERA_MOUSE TERA_MOUSE] Necessary for the fragmentation of Golgi stacks during mitosis and for their reassembly after mitosis. Involved in the formation of the transitional endoplasmic reticulum (tER). The transfer of membranes from the endoplasmic reticulum to the Golgi apparatus occurs via 50-70 nm transition vesicles which derive from part-rough, part-smooth transitional elements of the endoplasmic reticulum (tER). Vesicle budding from the tER is an ATP-dependent process. The ternary complex containing UFD1L, VCP and NPLOC4 binds ubiquitinated proteins and is necessary for the export of misfolded proteins from the ER to the cytoplasm, where they are degraded by the proteasome. The NPLOC4-UFD1L-VCP complex regulates spindle disassembly at the end of mitosis and is necessary for the formation of a closed nuclear envelope. Regulates E3 ubiquitin-protein ligase activity of RNF19A (By similarity). Component of the VCP/p97-AMFR/gp78 complex that participates in the final step of the sterol-mediated ubiquitination and endoplasmic reticulum-associated degradation (ERAD) of HMGCR. Also involved in DNA damage response: recruited to double-strand breaks (DSBs) sites in a RNF8- and RNF168-dependent manner and promotes the recruitment of TP53BP1 at DNA damage sites. Recruited to stalled replication forks by SPRTN: may act by mediating extraction of DNA polymerase eta (POLH) to prevent excessive translesion DNA synthesis and limit the incidence of mutations induced by DNA damage (By similarity).
+== 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/r7/1r7r_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=1r7r ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+p97/VCP is a member of the AAA ATPase family and has roles in both membrane fusion and ubiquitin dependent protein degradation. Here, we present a 3.6A crystal structure of murine p97 in which D2 domain has been modelled as poly-alanine and the remaining approximately 100 residues are absent. The resulting structure illustrates a head-to-tail packing arrangement of the two p97 AAA domains in a natural hexameric state with D1 ADP bound and D2 nucleotide free. The head-to-tail packing arrangement observed in this structure is in contrast to our previously predicted tail-to-tail packing model. The linker between the D1 and D2 domains is partially disordered, suggesting a flexible nature. Normal mode analysis of the crystal structure suggests anti-correlated motions and distinct conformational states of the two AAA domains.
-===The crystal structure of murine p97/VCP at 3.6A===
+The crystal structure of murine p97/VCP at 3.6A.,Huyton T, Pye VE, Briggs LC, Flynn TC, Beuron F, Kondo H, Ma J, Zhang X, Freemont PS J Struct Biol. 2003 Dec;144(3):337-48. PMID:14643202<ref>PMID:14643202</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_14643202}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 1r7r" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 14643202 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_14643202}}
+__TOC__
+</StructureSection>
-==About this Structure==
-R7R is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. The August 2006 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''AAA+ Proteases''  by David S. Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2006_8 10.2210/rcsb_pdb/mom_2006_8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1R7R OCA].
-==Reference==
-<ref group="xtra">PMID:14643202</ref><references group="xtra"/>
 [[Category: AAA+ Proteases]]
+[[Category: Large Structures]]
 [[Category: Mus musculus]]
 [[Category: RCSB PDB Molecule of the Month]]
-[[Category: Beuron, F.]]
+[[Category: Beuron F]]
-[[Category: Briggs, L C.]]
+[[Category: Briggs LC]]
-[[Category: Flynn, T C.]]
+[[Category: Flynn TC]]
-[[Category: Freemont, P S.]]
+[[Category: Freemont PS]]
-[[Category: Huyton, T.]]
+[[Category: Huyton T]]
-[[Category: Kondo, H.]]
+[[Category: Kondo H]]
-[[Category: Ma, J.]]
+[[Category: Ma J]]
-[[Category: Pye, V E.]]
+[[Category: Pye VE]]
-[[Category: Zhang, X.]]
+[[Category: Zhang X]]
-[[Category: Aaa]]
-[[Category: Cdc48]]
-[[Category: P97]]
-[[Category: Transport protein]]
-[[Category: Vcp]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 20 22:23:04 2010''