1yq0 - Revision history

OCA: Redirecting to 3cf1

OCA — Wed, 11 Jun 2008 08:16:39 GMT

Redirecting to 3cf1

←Older revision		Revision as of 08:16, 11 June 2008
Line 1:		Line 1:
-	[[~~Image:1yq0.gif\|left\|200px~~]]	+	#REDIRECT [[3cf1]] This PDB entry is obsolete and replaced by 3cf1
-		+
-	~~{{Structure~~	+
-	\|PDB~~= 1yq0 \|SIZE=350\|CAPTION= <scene name='initialview01'>1yq0</scene>, resolution 4.50Å~~	+
-	~~\|SITE=~~	+
-	~~\|LIGAND= <scene name='pdbligand=ADP:ADENOSINE-5'-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=AF3:ALUMINUM+FLUORIDE'>AF3</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>~~	+
-	~~\|ACTIVITY=~~	+
-	~~\|GENE= Vcp ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 Mus musculus])~~	+
-	~~\|DOMAIN=~~	+
-	~~\|RELATEDENTRY=[[1oz4\|1OZ4]], [[1ypw\|1YPW]]~~	+
-	\|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1yq0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yq0 OCA], [http://www.ebi.ac.uk/pdbsum/1yq0 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1yq0 RCSB]</span>	+
-	}}	+
-		+
-	~~'''Structure of p97/VCP in complex with ADP/ADP.AlFx'''~~	+
-		+
-		+
-	~~==Overview==~~	+
-	The AAA (ATPases associated with a variety of cellular activities) family of proteins bind, hydrolyze, and release ATP to effect conformational changes, assembly, or disassembly upon their binding partners and substrate molecules. One of the members of this family, the hexameric p97/valosin-containing protein p97/VCP, is ~~essential for the dislocation of misfolded membrane proteins from the endoplasmic reticulum. Here, we observe large motions~~ and dynamic changes of p97/VCP as it proceeds through the ATP hydrolysis cycle. The analysis is based on crystal structures of four representative ATP hydrolysis states: APO, AMP-PNP, hydrolysis transition state ADP x AlF3, and ADP bound. Two of the structures presented herein, ADP and AMP-PNP bound, are new structures, and the ADP x AlF3 structure was re-refined to higher resolution. The largest motions occur at two stages during the hydrolysis cycle: after, but not upon, nucleotide binding and then following nucleotide release. The motions occur primarily in the D2 domain, the D1 alpha-helical domain, and the N-terminal domain, relative to the relatively stationary and invariant D1alpha/beta domain. In addition to the motions, we observed a transition from a rigid state to a flexible state upon loss of the gamma-phosphate group, and a further increase in flexibility within the D2 domains upon nucleotide release. The domains within each protomer of the hexameric p97/VCP deviate from strict 6-fold symmetry, with the more flexible ADP state exhibiting greater asymmetry compared to the relatively rigid ADP x AlF3 state, suggesting a mechanism of action in which hydrolysis and conformational changes move about the hexamer in a processive fashion.	+
-		+
-	~~==About this Structure==~~	+
-	1YQ0 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YQ0 OCA].	+
-		+
-	~~==Reference==~~	+
-	~~Nucleotide dependent motion and mechanism of action of p97/VCP., DeLaBarre B, Brunger AT, J Mol Biol. 2005 Mar 25;347(2):437-52. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15740751 15740751]~~	+
-	~~[[Category: Mus musculus]]~~	+
-	~~[[Category: Single protein]]~~	+
-	~~[[Category: Brunger, A T.]]~~	+
-	~~[[Category: Delabarre, B.]]~~	+
-	~~[[Category: aaa]]~~	+
-	~~[[Category: atpase]]~~	+
-	~~[[Category: cdc48]]~~	+
-	~~[[Category: erad]]~~	+
-		+
-	~~''Page seeded~~ by ~~[http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 01:17:23 2008''~~	+

OCA at 22:17, 30 March 2008

OCA — Sun, 30 Mar 2008 22:17:34 GMT

←Older revision		Revision as of 22:17, 30 March 2008
Line 4:		Line 4:
	\|PDB= 1yq0 \|SIZE=350\|CAPTION= <scene name='initialview01'>1yq0</scene>, resolution 4.50Å		\|PDB= 1yq0 \|SIZE=350\|CAPTION= <scene name='initialview01'>1yq0</scene>, resolution 4.50Å
	\|SITE=		\|SITE=
-	\|LIGAND= ~~<scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>,~~ <scene name='pdbligand=ADP:ADENOSINE-5'-DIPHOSPHATE'>ADP</scene> ~~and~~ <scene name='pdbligand=AF3:ALUMINUM FLUORIDE'>AF3</scene>	+	\|LIGAND= <scene name='pdbligand=ADP:ADENOSINE-5'-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=AF3:ALUMINUM+FLUORIDE'>AF3</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>
	\|ACTIVITY=		\|ACTIVITY=
	\|GENE= Vcp ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 Mus musculus])		\|GENE= Vcp ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 Mus musculus])
		+	\|DOMAIN=
		+	\|RELATEDENTRY=[[1oz4\|1OZ4]], [[1ypw\|1YPW]]
		+	\|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1yq0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yq0 OCA], [http://www.ebi.ac.uk/pdbsum/1yq0 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1yq0 RCSB]</span>
	}}		}}

Line 24:		Line 27:
	[[Category: Brunger, A T.]]		[[Category: Brunger, A T.]]
	[[Category: Delabarre, B.]]		[[Category: Delabarre, B.]]
-	[[Category: ADP]]
-	[[Category: AF3]]
-	[[Category: ZN]]
	[[Category: aaa]]		[[Category: aaa]]
	[[Category: atpase]]		[[Category: atpase]]
Line 32:		Line 32:
	[[Category: erad]]		[[Category: erad]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun~~ Mar ~~23 14~~:23~~:05~~ 2008''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 01:17:23 2008''

OCA at 12:23, 23 March 2008

OCA — Sun, 23 Mar 2008 12:23:05 GMT

←Older revision		Revision as of 12:23, 23 March 2008
Line 4:		Line 4:
	\|PDB= 1yq0 \|SIZE=350\|CAPTION= <scene name='initialview01'>1yq0</scene>, resolution 4.50Å		\|PDB= 1yq0 \|SIZE=350\|CAPTION= <scene name='initialview01'>1yq0</scene>, resolution 4.50Å
	\|SITE=		\|SITE=
-	\|LIGAND= <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>, <scene name='pdbligand=ADP:ADENOSINE-5'-DIPHOSPHATE'>ADP</scene> and <scene name='pdbligand=AF3:ALUMINUM FLUORIDE'>AF3</scene>	+	\|LIGAND= <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>, <scene name='pdbligand=ADP:ADENOSINE-5'-DIPHOSPHATE'>ADP</scene> and <scene name='pdbligand=AF3:ALUMINUM FLUORIDE'>AF3</scene>
	\|ACTIVITY=		\|ACTIVITY=
	\|GENE= Vcp ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 Mus musculus])		\|GENE= Vcp ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 Mus musculus])
Line 32:		Line 32:
	[[Category: erad]]		[[Category: erad]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Thu~~ Mar ~~20 15~~:26:01 2008''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 23 14:23:05 2008''

OCA at 13:26, 20 March 2008

OCA — Thu, 20 Mar 2008 13:26:02 GMT

←Older revision		Revision as of 13:26, 20 March 2008
Line 1:		Line 1:
-	[[Image:1yq0.gif\|left\|200px]]~~<br /><applet load~~="1yq0~~" size~~="350~~" color~~=~~"white" frame="true" align="right" spinBox~~=~~"true"~~	+	[[Image:1yq0.gif\|left\|200px]]
-	~~caption="~~1yq0, resolution 4.50Å" />	+
-	'''Structure of p97/VCP in complex with ADP/ADP.AlFx'''~~<br />~~	+	{{Structure
		+	\|PDB= 1yq0 \|SIZE=350\|CAPTION= <scene name='initialview01'>1yq0</scene>, resolution 4.50Å
		+	\|SITE=
		+	\|LIGAND= <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>, <scene name='pdbligand=ADP:ADENOSINE-5'-DIPHOSPHATE'>ADP</scene> and <scene name='pdbligand=AF3:ALUMINUM FLUORIDE'>AF3</scene>
		+	\|ACTIVITY=
		+	\|GENE= Vcp ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 Mus musculus])
		+	}}
		+
		+	'''Structure of p97/VCP in complex with ADP/ADP.AlFx'''
		+

	==Overview==		==Overview==
Line 7:		Line 16:

	==About this Structure==		==About this Structure==
-	1YQ0 is a [~~http://en.wikipedia.org/wiki/Single_protein~~ Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus~~] with <scene name='pdbligand=ZN:'>ZN</scene>, <scene name='pdbligand=ADP:'>ADP</scene> and <scene name='pdbligand=AF3:'>AF3</scene> as [http://en.wikipedia.org/wiki/ligands ligands~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YQ0 OCA].	+	1YQ0 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YQ0 OCA].

	==Reference==		==Reference==
-	Nucleotide dependent motion and mechanism of action of p97/VCP., DeLaBarre B, Brunger AT, J Mol Biol. 2005 Mar 25;347(2):437-52. PMID:[http://~~ispc~~.~~weizmann~~.ac.~~il/~~/~~pmbin~~/~~getpm?pmid=~~15740751 15740751]	+	Nucleotide dependent motion and mechanism of action of p97/VCP., DeLaBarre B, Brunger AT, J Mol Biol. 2005 Mar 25;347(2):437-52. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15740751 15740751]
	[[Category: Mus musculus]]		[[Category: Mus musculus]]
	[[Category: Single protein]]		[[Category: Single protein]]
Line 23:		Line 32:
	[[Category: erad]]		[[Category: erad]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu ~~Feb 21 16~~:07:53 2008''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 15:26:01 2008''

OCA at 14:07, 21 February 2008

OCA — Thu, 21 Feb 2008 14:07:54 GMT

←Older revision		Revision as of 14:07, 21 February 2008
Line 1:		Line 1:
-	[[Image:1yq0.gif\|left\|200px]]<br /><applet load="1yq0" size="~~450~~" color="white" frame="true" align="right" spinBox="true"	+	[[Image:1yq0.gif\|left\|200px]]<br /><applet load="1yq0" size="350" color="white" frame="true" align="right" spinBox="true"
	caption="1yq0, resolution 4.50Å" />		caption="1yq0, resolution 4.50Å" />
	'''Structure of p97/VCP in complex with ADP/ADP.AlFx'''<br />		'''Structure of p97/VCP in complex with ADP/ADP.AlFx'''<br />

	==Overview==		==Overview==
-	The AAA (ATPases associated with a variety of cellular activities) family, of proteins bind, hydrolyze, and release ATP to effect conformational, changes, assembly, or disassembly upon their binding partners and, substrate molecules. One of the members of this family, the hexameric, p97/valosin-containing protein p97/VCP, is essential for the dislocation, of misfolded membrane proteins from the endoplasmic reticulum. Here, we, observe large motions and dynamic changes of p97/VCP as it proceeds, through the ATP hydrolysis cycle. The analysis is based on crystal, structures of four representative ATP hydrolysis states: APO, AMP-PNP, hydrolysis transition state ADP x AlF3, and ADP bound. Two of the, structures presented herein, ADP and AMP-PNP bound, are new structures, and the ADP x AlF3 structure was re-refined to higher resolution. The, largest motions occur at two stages during the hydrolysis cycle: after, but not upon, nucleotide binding and then following nucleotide release., The motions occur primarily in the D2 domain, the D1 alpha-helical domain, and the N-terminal domain, relative to the relatively stationary and, invariant D1alpha/beta domain. In addition to the motions, we observed a, transition from a rigid state to a flexible state upon loss of the, gamma-phosphate group, and a further increase in flexibility within the D2, domains upon nucleotide release. The domains within each protomer of the, hexameric p97/VCP deviate from strict 6-fold symmetry, with the more, flexible ADP state exhibiting greater asymmetry compared to the relatively, rigid ADP x AlF3 state, suggesting a mechanism of action in which, hydrolysis and conformational changes move about the hexamer in a, processive fashion.	+	The AAA (ATPases associated with a variety of cellular activities) family of proteins bind, hydrolyze, and release ATP to effect conformational changes, assembly, or disassembly upon their binding partners and substrate molecules. One of the members of this family, the hexameric p97/valosin-containing protein p97/VCP, is essential for the dislocation of misfolded membrane proteins from the endoplasmic reticulum. Here, we observe large motions and dynamic changes of p97/VCP as it proceeds through the ATP hydrolysis cycle. The analysis is based on crystal structures of four representative ATP hydrolysis states: APO, AMP-PNP, hydrolysis transition state ADP x AlF3, and ADP bound. Two of the structures presented herein, ADP and AMP-PNP bound, are new structures, and the ADP x AlF3 structure was re-refined to higher resolution. The largest motions occur at two stages during the hydrolysis cycle: after, but not upon, nucleotide binding and then following nucleotide release. The motions occur primarily in the D2 domain, the D1 alpha-helical domain, and the N-terminal domain, relative to the relatively stationary and invariant D1alpha/beta domain. In addition to the motions, we observed a transition from a rigid state to a flexible state upon loss of the gamma-phosphate group, and a further increase in flexibility within the D2 domains upon nucleotide release. The domains within each protomer of the hexameric p97/VCP deviate from strict 6-fold symmetry, with the more flexible ADP state exhibiting greater asymmetry compared to the relatively rigid ADP x AlF3 state, suggesting a mechanism of action in which hydrolysis and conformational changes move about the hexamer in a processive fashion.

	==About this Structure==		==About this Structure==
-	1YQ0 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus] with ZN, ADP and AF3 as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://~~ispc~~.weizmann.ac.il/oca-bin/ocashort?id=1YQ0 OCA].	+	1YQ0 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus] with <scene name='pdbligand=ZN:'>ZN</scene>, <scene name='pdbligand=ADP:'>ADP</scene> and <scene name='pdbligand=AF3:'>AF3</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YQ0 OCA].

	==Reference==		==Reference==
Line 13:		Line 13:
	[[Category: Mus musculus]]		[[Category: Mus musculus]]
	[[Category: Single protein]]		[[Category: Single protein]]
-	[[Category: Brunger, A.T.]]	+	[[Category: Brunger, A T.]]
	[[Category: Delabarre, B.]]		[[Category: Delabarre, B.]]
	[[Category: ADP]]		[[Category: ADP]]
Line 23:		Line 23:
	[[Category: erad]]		[[Category: erad]]

-	''Page seeded by [http://~~ispc~~.weizmann.ac.il/oca OCA ] on ~~Wed Nov~~ 21 06:58:~~44 2007~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:07:53 2008''

OCA: New page: 200px
'''Structure of p97/VCP...
OCA — Wed, 21 Nov 2007 04:51:29 GMT

New page: 200px<br /><applet load="1yq0" size="450" color="white" frame="true" align="right" spinBox="true" caption="1yq0, resolution 4.50Å" /> '''Structure of p97/VCP...

New page
[[Image:1yq0.gif|left|200px]]<br /><applet load="1yq0" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1yq0, resolution 4.50Å" />
'''Structure of p97/VCP in complex with ADP/ADP.AlFx'''<br />

==Overview==
The AAA (ATPases associated with a variety of cellular activities) family, of proteins bind, hydrolyze, and release ATP to effect conformational, changes, assembly, or disassembly upon their binding partners and, substrate molecules. One of the members of this family, the hexameric, p97/valosin-containing protein p97/VCP, is essential for the dislocation, of misfolded membrane proteins from the endoplasmic reticulum. Here, we, observe large motions and dynamic changes of p97/VCP as it proceeds, through the ATP hydrolysis cycle. The analysis is based on crystal, structures of four representative ATP hydrolysis states: APO, AMP-PNP, hydrolysis transition state ADP x AlF3, and ADP bound. Two of the, structures presented herein, ADP and AMP-PNP bound, are new structures, and the ADP x AlF3 structure was re-refined to higher resolution. The, largest motions occur at two stages during the hydrolysis cycle: after, but not upon, nucleotide binding and then following nucleotide release., The motions occur primarily in the D2 domain, the D1 alpha-helical domain, and the N-terminal domain, relative to the relatively stationary and, invariant D1alpha/beta domain. In addition to the motions, we observed a, transition from a rigid state to a flexible state upon loss of the, gamma-phosphate group, and a further increase in flexibility within the D2, domains upon nucleotide release. The domains within each protomer of the, hexameric p97/VCP deviate from strict 6-fold symmetry, with the more, flexible ADP state exhibiting greater asymmetry compared to the relatively, rigid ADP x AlF3 state, suggesting a mechanism of action in which, hydrolysis and conformational changes move about the hexamer in a, processive fashion.

==About this Structure==
1YQ0 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus] with ZN, ADP and AF3 as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1YQ0 OCA].

==Reference==
Nucleotide dependent motion and mechanism of action of p97/VCP., DeLaBarre B, Brunger AT, J Mol Biol. 2005 Mar 25;347(2):437-52. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15740751 15740751]
[[Category: Mus musculus]]
[[Category: Single protein]]
[[Category: Brunger, A.T.]]
[[Category: Delabarre, B.]]
[[Category: ADP]]
[[Category: AF3]]
[[Category: ZN]]
[[Category: aaa]]
[[Category: atpase]]
[[Category: cdc48]]
[[Category: erad]]

''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 06:58:44 2007''