3cf1

From Proteopedia

(Difference between revisions)

Revision as of 12:12, 8 February 2016

Structure of P97/vcp in complex with ADP/ADP.alfx

Structural highlights

3cf1 is a 3 chain structure with sequence from Lk3 transgenic mice. This structure supersedes the now removed PDB entries 1oz4 and 1yq0. 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:	,
Related:	1oz4, 1yq0, 3cf2, 3cf3
Gene:	Vcp (LK3 transgenic mice)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum

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

The ATPases associated with various cellular activities (AAA) protein p97 has been implicated in a variety of cellular processes, including endoplasmic reticulum-associated degradation and homotypic membrane fusion. p97 belongs to a subgroup of AAA proteins that contains two nucleotide binding domains, D1 and D2. We determined the crystal structure of D2 at 3.0 A resolution. This model enabled rerefinement of full-length p97 in different nucleotide states against previously reported low-resolution diffraction data to significantly improved R values and Ramachandran statistics. Although the overall fold remained similar, there are significant improvements, especially around the D2 nucleotide binding site. The rerefinement illustrates the importance of knowledge of high-resolution structures of fragments covering most of the whole molecule. The structures suggest that nucleotide hydrolysis is transformed into larger conformational changes by pushing of one D2 domain by its neighbor in the hexamer, and transmission of nucleotide-state information through the D1-D2 linker to displace the N-terminal, effector binding domain.

Improved structures of full-length p97, an AAA ATPase: implications for mechanisms of nucleotide-dependent conformational change.,Davies JM, Brunger AT, Weis WI Structure. 2008 May;16(5):715-26. PMID:18462676^[1]

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

References

↑ Davies JM, Brunger AT, Weis WI. Improved structures of full-length p97, an AAA ATPase: implications for mechanisms of nucleotide-dependent conformational change. Structure. 2008 May;16(5):715-26. PMID:18462676 doi:http://dx.doi.org/10.1016/j.str.2008.02.010

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3cf1"

@@ Line 2: / Line 2: @@
 <StructureSection load='3cf1' size='340' side='right' caption='[[3cf1]], [[Resolution|resolution]] 4.40&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3cf1]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. This structure supersedes the now removed PDB entries  and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1yq0 1yq0]. 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=3CF1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3CF1 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3cf1]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1oz4 1oz4] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1yq0 1yq0]. 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=3CF1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3CF1 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>, <scene name='pdbligand=AF3:ALUMINUM+FLUORIDE'>AF3</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1oz4|1oz4]], [[1yq0|1yq0]], [[3cf2|3cf2]], [[3cf3|3cf3]]</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 Mus musculus])</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=3cf1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cf1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3cf1 RCSB], [http://www.ebi.ac.uk/pdbsum/3cf1 PDBsum]</span></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=3cf1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cf1 OCA], [http://pdbe.org/3cf1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3cf1 RCSB], [http://www.ebi.ac.uk/pdbsum/3cf1 PDBsum]</span></td></tr>
 </table>
 == Function ==
@@ Line 18: / Line 18: @@
     <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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=3cf1 ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 28: / Line 28: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 3cf1" style="background-color:#fffaf0;"></div>
 ==See Also==
@@ Line 36: / Line 37: @@
 </StructureSection>
 [[Category: AAA+ Proteases]]
-[[Category: Mus musculus]]
+[[Category: Lk3 transgenic mice]]
 [[Category: RCSB PDB Molecule of the Month]]
 [[Category: Brunger, A T]]

3cf1

From Proteopedia

Revision as of 12:12, 8 February 2016

Structure of P97/vcp in complex with ADP/ADP.alfx

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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