3qfp: Difference between revisions

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[[~~Image~~:~~3qfp~~.~~png~~|~~left~~|~~200px~~]]

==Crystal structure of yeast Hsp70 (Bip/Kar2) ATPase domain==

== Structural highlights ==

<table><tr><td colspan='2'>[[3qfp]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QFP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3QFP FirstGlance]. <br>

</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene><br>

<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3qfu|3qfu]], [[3qml|3qml]]</td></tr>

<tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">KAR2, GRP78, SSD1, YJL034W, J1248 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])</td></tr>

<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3qfp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qfp OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3qfp RCSB], [http://www.ebi.ac.uk/pdbsum/3qfp PDBsum]</span></td></tr>

<table>

== Publication Abstract from PubMed ==

Sil1 functions as a nucleotide exchange factor (NEF) for Bip in eukaryotic cells. In order to understand how Sil1 functions as a NEF, we analyzed the crystal structure of the yeast Bip-Sil1 complex at a resolution of 2.3A. In the complex, the Sil1 molecule acts as a "molecular clamp" which binds to the IIb lobe of the Bip ATPase domain. Sil1 binding causes lobe IIb to rotate ~13.5 degrees away from the ADP-binding pocket and lobe Ib to rotate in the opposite direction for ~3.7 degrees . These conformational changes in Bip open up the nucleotide-binding pocket in the ATPase domain and simultaneously disrupt the hydrogen bonds between Bip and bound ADP, thus providing a mechanism for ADP release. We also demonstrate that Sil1 mutations that disrupt binding to the Bip ATPase domain abolish Sil1's ability to stimulate Bip ATPase activity.

<!--

Structural analysis of the Sil1-Bip complex reveals how Sil1 functions as a nucleotide exchange factor.,Yan M, Li J, Sha B Biochem J. 2011 Jun 15. PMID:21675960<ref>PMID:21675960</ref>

~~The line below this paragraph~~, ~~containing "STRUCTURE_3qfp"~~, ~~creates the "Structure Box" on the page~~.

~~You may change the PDB parameter (which sets the PDB file loaded into the applet)~~

~~or the SCENE parameter (which sets the initial scene displayed when the page is loaded),~~

~~or leave the SCENE parameter empty for the default display~~.

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~~{{STRUCTURE_3qfp| PDB=3qfp | SCENE= }}~~

~~===Crystal structure of yeast Hsp70 (Bip~~/~~Kar2) ATPase domain===~~

From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>

</div>

== References ==

~~<!--~~

~~The line below this paragraph~~, ~~{{ABSTRACT_PUBMED_21675960}}, adds~~ the ~~Publication Abstract to the page~~

__TOC__

~~(as it appears on PubMed at http://www~~.~~pubmed~~.~~gov), where 21675960 is the PubMed ID number~~.

</StructureSection>

-->

~~{{ABSTRACT_PUBMED_21675960}}~~

~~==About this Structure==~~

~~[[3qfp]] is a 1 chain structure with sequence from [http:~~/~~/en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QFP OCA].~~

==~~Reference~~==

<~~ref group="xtra">PMID:021675960<~~/~~ref~~><~~references group="xtra"~~/>

[[Category: Saccharomyces cerevisiae]]

[[Category: Li, J Z.]]

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@@ Line 1: / Line 1: @@
-[[Image:3qfp.png|left|200px]]
+==Crystal structure of yeast Hsp70 (Bip/Kar2) ATPase domain==
+<StructureSection load='3qfp' size='340' side='right' caption='[[3qfp]], [[Resolution|resolution]] 2.26&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[3qfp]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QFP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3QFP FirstGlance]. <br>
+</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene><br>
+<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3qfu|3qfu]], [[3qml|3qml]]</td></tr>
+<tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">KAR2, GRP78, SSD1, YJL034W, J1248 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])</td></tr>
+<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3qfp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qfp OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3qfp RCSB], [http://www.ebi.ac.uk/pdbsum/3qfp PDBsum]</span></td></tr>
+<table>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Sil1 functions as a nucleotide exchange factor (NEF) for Bip in eukaryotic cells. In order to understand how Sil1 functions as a NEF, we analyzed the crystal structure of the yeast Bip-Sil1 complex at a resolution of 2.3A. In the complex, the Sil1 molecule acts as a "molecular clamp" which binds to the IIb lobe of the Bip ATPase domain. Sil1 binding causes lobe IIb to rotate ~13.5 degrees away from the ADP-binding pocket and lobe Ib to rotate in the opposite direction for ~3.7 degrees . These conformational changes in Bip open up the nucleotide-binding pocket in the ATPase domain and simultaneously disrupt the hydrogen bonds between Bip and bound ADP, thus providing a mechanism for ADP release. We also demonstrate that Sil1 mutations that disrupt binding to the Bip ATPase domain abolish Sil1's ability to stimulate Bip ATPase activity.
-<!--
+Structural analysis of the Sil1-Bip complex reveals how Sil1 functions as a nucleotide exchange factor.,Yan M, Li J, Sha B Biochem J. 2011 Jun 15. PMID:21675960<ref>PMID:21675960</ref>
-The line below this paragraph, containing "STRUCTURE_3qfp", creates the "Structure Box" on the page.
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-or leave the SCENE parameter empty for the default display.
--->
-{{STRUCTURE_3qfp|  PDB=3qfp  |  SCENE=  }}
-===Crystal structure of yeast Hsp70 (Bip/Kar2) ATPase domain===
+From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
+</div>
+== References ==
-<!--
+<references/>
-The line below this paragraph, {{ABSTRACT_PUBMED_21675960}}, adds the Publication Abstract to the page
+__TOC__
-(as it appears on PubMed at http://www.pubmed.gov), where 21675960 is the PubMed ID number.
+</StructureSection>
--->
-{{ABSTRACT_PUBMED_21675960}}
-==About this Structure==
-[[3qfp]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QFP OCA].
-==Reference==
-<ref group="xtra">PMID:021675960</ref><references group="xtra"/>
 [[Category: Saccharomyces cerevisiae]]
 [[Category: Li, J Z.]]