1r7r

From Proteopedia

(Difference between revisions)

Revision as of 13:20, 16 December 2020

The crystal structure of murine p97/VCP at 3.6A

Structural highlights

1r7r is a 1 chain structure with sequence from Lk3 transgenic mice. The August 2006 RCSB PDB Molecule of the Month feature on AAA+ Proteases by David S. Goodsell is 10.2210/rcsb_pdb/mom_2006_8. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Gene:	VCP (LK3 transgenic mice)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[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

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

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.,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^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Huyton T, Pye VE, Briggs LC, Flynn TC, Beuron F, Kondo H, Ma J, Zhang X, Freemont PS. The crystal structure of murine p97/VCP at 3.6A. J Struct Biol. 2003 Dec;144(3):337-48. PMID:14643202

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1r7r"

@@ Line 1: / Line 1: @@
 ==The crystal structure of murine p97/VCP at 3.6A==
-<StructureSection load='1r7r' size='340' side='right' caption='[[1r7r]], [[Resolution|resolution]] 3.60&Aring;' scene=''>
+<StructureSection load='1r7r' size='340' side='right'caption='[[1r7r]], [[Resolution|resolution]] 3.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1r7r]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. 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]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1R7R FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1r7r]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. 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]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1R7R FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene></td></tr>
+</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>
 <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">VCP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice])</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1r7r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1r7r OCA], [http://pdbe.org/1r7r PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1r7r RCSB], [http://www.ebi.ac.uk/pdbsum/1r7r PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1r7r ProSAT]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1r7r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1r7r OCA], [http://pdbe.org/1r7r PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1r7r RCSB], [http://www.ebi.ac.uk/pdbsum/1r7r PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1r7r ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 14: / Line 14: @@
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/r7/1r7r_consurf.spt"</scriptWhenChecked>
+    <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>
@@ Line 34: / Line 34: @@
 </StructureSection>
 [[Category: AAA+ Proteases]]
+[[Category: Large Structures]]
 [[Category: Lk3 transgenic mice]]
 [[Category: RCSB PDB Molecule of the Month]]

1r7r

From Proteopedia

Revision as of 13:20, 16 December 2020

The crystal structure of murine p97/VCP at 3.6A

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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